HaplotypeCaller on Spark
This is an implementation of {@link HaplotypeCaller} using spark to distribute the computation. It is still in an early stage of development and does not yet support all the options that the non-spark version does. Specifically it does not support the --dbsnp, --comp, and --bam-output options.
gatk HaplotypeCallerSpark \ -R Homo_sapiens_assembly38.fasta \ -I input.bam \ -O output.vcf.gz
These Read Filters are automatically applied to the data by the Engine before processing by HaplotypeCallerSpark.
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Arguments | |||
| --input -I |
BAM/SAM/CRAM file containing reads | ||
| --output -O |
Single file to which variants should be written | ||
| --reference -R |
Reference sequence file | ||
| Optional Tool Arguments | |||
| --alleles |
The set of alleles to force-call regardless of evidence | ||
| --annotate-with-num-discovered-alleles |
false | If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site | |
| --annotation -A |
One or more specific annotations to add to variant calls | ||
| --annotation-group -G |
One or more groups of annotations to apply to variant calls | ||
| --annotations-to-exclude -AX |
One or more specific annotations to exclude from variant calls | ||
| --arguments_file |
read one or more arguments files and add them to the command line | ||
| --assembly-region-padding |
100 | Number of additional bases of context to include around each assembly region | |
| --bam-partition-size |
0 | maximum number of bytes to read from a file into each partition of reads. Setting this higher will result in fewer partitions. Note that this will not be equal to the size of the partition in memory. Defaults to 0, which uses the default split size (determined by the Hadoop input format, typically the size of one HDFS block). | |
| --base-quality-score-threshold |
18 | Base qualities below this threshold will be reduced to the minimum (6) | |
| --conf |
Spark properties to set on the Spark context in the format |
||
| --contamination-fraction-to-filter -contamination |
0.0 | Fraction of contamination in sequencing data (for all samples) to aggressively remove | |
| --dbsnp -D |
dbSNP file | ||
| --disable-sequence-dictionary-validation |
false | If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk! | |
| --dont-use-dragstr-pair-hmm-scores |
false | disable DRAGstr pair-hmm score even when dragstr-params-path was provided | |
| --dont-use-soft-clipped-bases |
false | Do not analyze soft clipped bases in the reads | |
| --dragen-mode |
false | Single argument for enabling the bulk of DRAGEN-GATK features. NOTE: THIS WILL OVERWRITE PROVIDED ARGUMENT CHECK TOOL INFO TO SEE WHICH ARGUMENTS ARE SET). | |
| --dragstr-het-hom-ratio |
2 | het to hom prior ratio use with DRAGstr on | |
| --dragstr-params-path |
location of the DRAGstr model parameters for STR error correction used in the Pair HMM. When provided, it overrides other PCR error correcting mechanisms | ||
| --enable-dynamic-read-disqualification-for-genotyping |
false | Will enable less strict read disqualification low base quality reads | |
| --flow-order-for-annotations |
flow order used for this annotations. [readGroup:]flowOrder | ||
| --founder-id |
Samples representing the population "founders" | ||
| --gcs-max-retries -gcs-retries |
20 | If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection | |
| --gcs-project-for-requester-pays |
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed. | ||
| --genotype-assignment-method -gam |
USE_PLS_TO_ASSIGN | How we assign genotypes | |
| --graph-output -graph |
Write debug assembly graph information to this file | ||
| --help -h |
false | display the help message | |
| --heterozygosity |
0.001 | Heterozygosity value used to compute prior probabilities for any locus. See the GATKDocs for full details on the meaning of this population genetics concept | |
| --heterozygosity-stdev |
0.01 | Standard deviation of heterozygosity for SNP and indel calling. | |
| --indel-heterozygosity |
1.25E-4 | Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept | |
| --interval-merging-rule -imr |
ALL | Interval merging rule for abutting intervals | |
| --intervals -L |
One or more genomic intervals over which to operate | ||
| --max-assembly-region-size |
300 | Maximum size of an assembly region | |
| --max-reads-per-alignment-start |
50 | Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to 0 to disable. | |
| --min-assembly-region-size |
50 | Minimum size of an assembly region | |
| --min-base-quality-score -mbq |
10 | Minimum base quality required to consider a base for calling | |
| --native-pair-hmm-threads |
4 | How many threads should a native pairHMM implementation use | |
| --native-pair-hmm-use-double-precision |
false | use double precision in the native pairHmm. This is slower but matches the java implementation better | |
| --num-reducers |
0 | For tools that shuffle data or write an output, sets the number of reducers. Defaults to 0, which gives one partition per 10MB of input. | |
| --num-reference-samples-if-no-call |
0 | Number of hom-ref genotypes to infer at sites not present in a panel | |
| --output-mode |
EMIT_VARIANTS_ONLY | Specifies which type of calls we should output | |
| --output-shard-tmp-dir |
when writing a bam, in single sharded mode this directory to write the temporary intermediate output shards, if not specified .parts/ will be used | ||
| --pedigree -ped |
Pedigree file for determining the population "founders" | ||
| --ploidy-regions |
Interval file with column specifying desired ploidy for genotyping models. Overrides default ploidy and user-provided --ploidy argument in specific regions. | ||
| --population-callset -population |
Callset to use in calculating genotype priors | ||
| --program-name |
Name of the program running | ||
| --read-shard-padding |
100 | Each read shard has this many bases of extra context on each side. Read shards must have as much or more padding than assembly regions. | |
| --read-shard-size |
5000 | Maximum size of each read shard, in bases. For good performance, this should be much larger than the maximum assembly region size. | |
| --recover-dangling-heads |
false | (Deprecated) This argument is deprecated since version 3.3 | |
| --sample-name -ALIAS |
Name of single sample to use from a multi-sample bam | ||
| --sample-ploidy -ploidy |
2 | Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy). | |
| --sharded-output |
false | For tools that write an output, write the output in multiple pieces (shards) | |
| --shuffle |
false | whether to use the shuffle implementation or not | |
| --spark-master |
local[*] | URL of the Spark Master to submit jobs to when using the Spark pipeline runner. | |
| --spark-verbosity |
Spark verbosity. Overrides --verbosity for Spark-generated logs only. Possible values: {ALL, DEBUG, INFO, WARN, ERROR, FATAL, OFF, TRACE} | ||
| --standard-min-confidence-threshold-for-calling -stand-call-conf |
30.0 | The minimum phred-scaled confidence threshold at which variants should be called | |
| --strict |
false | whether to use the strict implementation or not (defaults to the faster implementation that doesn't strictly match the walker version) | |
| --use-new-qual-calculator -new-qual |
true | (Deprecated) Use the new AF model instead of the so-called exact model | |
| --use-nio |
false | Whether to use NIO or the Hadoop filesystem (default) for reading files. (Note that the Hadoop filesystem is always used for writing files.) | |
| --use-pdhmm |
false | Partially Determined HMM, an alternative to the regular assembly haplotypes where we instead construct artificial haplotypes out of the union of the assembly and pileup alleles. | |
| --use-posteriors-to-calculate-qual -gp-qual |
false | if available, use the genotype posterior probabilities to calculate the site QUAL | |
| --version |
false | display the version number for this tool | |
| Optional Common Arguments | |||
| --add-output-vcf-command-line |
true | If true, adds a command line header line to created VCF files. | |
| --create-output-bam-index -OBI |
true | If true, create a BAM index when writing a coordinate-sorted BAM file. | |
| --create-output-bam-splitting-index |
true | If true, create a BAM splitting index (SBI) when writing a coordinate-sorted BAM file. | |
| --create-output-variant-index -OVI |
true | If true, create a VCF index when writing a coordinate-sorted VCF file. | |
| --disable-read-filter -DF |
Read filters to be disabled before analysis | ||
| --disable-tool-default-read-filters |
false | Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on) | |
| --exclude-intervals -XL |
One or more genomic intervals to exclude from processing | ||
| --gatk-config-file |
A configuration file to use with the GATK. | ||
| --interval-exclusion-padding -ixp |
0 | Amount of padding (in bp) to add to each interval you are excluding. | |
| --interval-padding -ip |
0 | Amount of padding (in bp) to add to each interval you are including. | |
| --interval-set-rule -isr |
UNION | Set merging approach to use for combining interval inputs | |
| --inverted-read-filter -XRF |
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters). | ||
| --QUIET |
false | Whether to suppress job-summary info on System.err. | |
| --read-filter -RF |
Read filters to be applied before analysis | ||
| --read-index |
Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically. | ||
| --read-validation-stringency -VS |
SILENT | Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. | |
| --splitting-index-granularity |
4096 | Granularity to use when writing a splitting index, one entry will be put into the index every n reads where n is this granularity value. Smaller granularity results in a larger index with more available split points. | |
| --tmp-dir |
Temp directory to use. | ||
| --use-jdk-deflater -jdk-deflater |
false | Whether to use the JdkDeflater (as opposed to IntelDeflater) | |
| --use-jdk-inflater -jdk-inflater |
false | Whether to use the JdkInflater (as opposed to IntelInflater) | |
| --verbosity |
INFO | Control verbosity of logging. | |
| Advanced Arguments | |||
| --active-probability-threshold |
0.002 | Minimum probability for a locus to be considered active. | |
| --adaptive-pruning |
false | Use Mutect2's adaptive graph pruning algorithm | |
| --adaptive-pruning-initial-error-rate |
0.001 | Initial base error rate estimate for adaptive pruning | |
| --all-site-pls |
false | Annotate all sites with PLs | |
| --allele-informative-reads-overlap-margin |
2 | Likelihood and read-based annotations will only take into consideration reads that overlap the variant or any base no further than this distance expressed in base pairs | |
| --allow-non-unique-kmers-in-ref |
false | Allow graphs that have non-unique kmers in the reference | |
| --apply-bqd |
false | If enabled this argument will apply the DRAGEN-GATK BaseQualityDropout model to the genotyping model for filtering sites due to Linked Error mode. | |
| --apply-frd |
false | If enabled this argument will apply the DRAGEN-GATK ForeignReadDetection model to the genotyping model for filtering sites. | |
| --bam-output -bamout |
File to which assembled haplotypes should be written | ||
| --bam-writer-type |
CALLED_HAPLOTYPES | Which haplotypes should be written to the BAM | |
| --comparison -comp |
Comparison VCF file(s) | ||
| --contamination-fraction-per-sample-file -contamination-file |
Tab-separated File containing fraction of contamination in sequencing data (per sample) to aggressively remove. Format should be " |
||
| --debug-assembly -debug |
false | Print out verbose debug information about each assembly region | |
| --disable-cap-base-qualities-to-map-quality |
false | If false this disables capping of base qualities in the HMM to the mapping quality of the read | |
| --disable-optimizations |
false | Don't skip calculations in ActiveRegions with no variants | |
| --disable-spanning-event-genotyping |
false | If enabled this argument will disable inclusion of the '*' spanning event when genotyping events that overlap deletions | |
| --disable-symmetric-hmm-normalizing |
false | Toggle to revive legacy behavior of asymmetrically normalizing the arguments to the reference haplotype | |
| --disable-tool-default-annotations |
false | Disable all tool default annotations | |
| --do-not-correct-overlapping-quality |
false | Disable overlapping base quality correction | |
| --do-not-run-physical-phasing |
false | Disable physical phasing | |
| --dont-increase-kmer-sizes-for-cycles |
false | Disable iterating over kmer sizes when graph cycles are detected | |
| --dont-use-dragstr-priors |
false | Forfeit the use of the DRAGstr model to calculate genotype priors. This argument does not have any effect in the absence of DRAGstr model parameters (--dragstr-model-params) | |
| --dragen-378-concordance-mode |
false | Single argument for enabling the bulk of DRAGEN-GATK features including new developments for concordance against DRAGEN 3.7.8. NOTE: THIS WILL OVERWRITE PROVIDED ARGUMENT CHECK TOOL INFO TO SEE WHICH ARGUMENTS ARE SET). | |
| --emit-ref-confidence -ERC |
NONE | Mode for emitting reference confidence scores (For Mutect2, this is a BETA feature) | |
| --enable-all-annotations |
false | Use all possible annotations (not for the faint of heart) | |
| --expected-mismatch-rate-for-read-disqualification |
0.02 | Error rate used to set expectation for post HMM read disqualification based on mismatches | |
| --floor-blocks |
false | Output the band lower bound for each GQ block regardless of the data it represents | |
| --flow-assembly-collapse-partial-mode |
false | Collapse long flow-based hmers only up to difference in reference | |
| --flow-disallow-probs-larger-than-call |
false | Cap probabilities of error to 1 relative to base call | |
| --flow-fill-empty-bins-value |
0.001 | Value to fill the zeros of the matrix with | |
| --flow-filter-alleles |
false | pre-filter alleles before genotyping | |
| --flow-filter-alleles-qual-threshold |
30.0 | Threshold for prefiltering alleles on quality | |
| --flow-filter-alleles-sor-threshold |
3.0 | Threshold for prefiltering alleles on SOR | |
| --flow-filter-lone-alleles |
false | Remove also lone alleles during allele filtering | |
| --flow-lump-probs |
false | Should all probabilities of insertion or deletion in the flow be combined together | |
| --flow-matrix-mods |
Modifications instructions to the read flow matrix. Format is src,dst{,src,dst}+. Example: 10,12,11,12 - these instructions will copy element 10 into 11 and 12 | ||
| --flow-mode |
NONE | Single argument for enabling the bulk of Flow Based features. NOTE: THIS WILL OVERWRITE PROVIDED ARGUMENT CHECK TOOL INFO TO SEE WHICH ARGUMENTS ARE SET). | |
| --flow-probability-scaling-factor |
10 | probability scaling factor for (phred=10) for probability quantization | |
| --flow-quantization-bins |
121 | Number of bins for probability quantization | |
| --flow-remove-non-single-base-pair-indels |
false | Should the probabilities of more then 1 indel be used | |
| --flow-remove-one-zero-probs |
false | Remove probabilities of basecall of zero from non-zero genome | |
| --flow-report-insertion-or-deletion |
false | Report either insertion or deletion, probability, not both | |
| --flow-retain-max-n-probs-base-format |
false | Keep only hmer/2 probabilities (like in base format) | |
| --flow-symmetric-indel-probs |
false | Should indel probabilities be symmetric in flow | |
| --flow-use-t0-tag |
false | Use t0 tag if exists in the read to create flow matrix | |
| --force-active |
false | If provided, all regions will be marked as active | |
| --force-call-filtered-alleles -genotype-filtered-alleles |
false | Force-call filtered alleles included in the resource specified by --alleles | |
| --gvcf-gq-bands -GQB |
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] | Exclusive upper bounds for reference confidence GQ bands (must be in [1, 100] and specified in increasing order) | |
| --indel-size-to-eliminate-in-ref-model |
10 | The size of an indel to check for in the reference model | |
| --keep-boundary-flows |
false | prevent spreading of boundary flows. | |
| --kmer-size |
[10, 25] | Kmer size to use in the read threading assembler | |
| --likelihood-calculation-engine |
PairHMM | What likelihood calculation engine to use to calculate the relative likelihood of reads vs haplotypes | |
| --linked-de-bruijn-graph |
false | If enabled, the Assembly Engine will construct a Linked De Bruijn graph to recover better haplotypes | |
| --mapping-quality-threshold-for-genotyping |
20 | Control the threshold for discounting reads from the genotyper due to mapping quality after the active region detection and assembly steps but before genotyping. NOTE: this is in contrast to the --minimum-mapping-quality argument which filters reads from all parts of the HaplotypeCaller. If you would like to call genotypes with a different threshold both arguments must be set. | |
| --max-alternate-alleles |
6 | Maximum number of alternate alleles to genotype | |
| --max-effective-depth-adjustment-for-frd |
0 | Set the maximum depth to modify FRD adjustment to in the event of high depth sites (0 to disable) | |
| --max-genotype-count |
1024 | Maximum number of genotypes to consider at any site | |
| --max-mnp-distance -mnp-dist |
0 | Two or more phased substitutions separated by this distance or less are merged into MNPs. | |
| --max-num-haplotypes-in-population |
128 | Maximum number of haplotypes to consider for your population | |
| --max-prob-propagation-distance |
50 | Upper limit on how many bases away probability mass can be moved around when calculating the boundaries between active and inactive assembly regions | |
| --max-unpruned-variants |
100 | Maximum number of variants in graph the adaptive pruner will allow | |
| --min-dangling-branch-length |
4 | Minimum length of a dangling branch to attempt recovery | |
| --min-pruning |
2 | Minimum support to not prune paths in the graph | |
| --num-pruning-samples |
1 | Number of samples that must pass the minPruning threshold | |
| --pair-hmm-gap-continuation-penalty |
10 | Flat gap continuation penalty for use in the Pair HMM | |
| --pair-hmm-implementation -pairHMM |
FASTEST_AVAILABLE | The PairHMM implementation to use for genotype likelihood calculations | |
| --pair-hmm-results-file |
File to write exact pairHMM inputs/outputs to for debugging purposes | ||
| --pcr-indel-model |
CONSERVATIVE | The PCR indel model to use | |
| --phred-scaled-global-read-mismapping-rate |
45 | The global assumed mismapping rate for reads | |
| --pileup-detection |
false | If enabled, the variant caller will create pileup-based haplotypes in addition to the assembly-based haplotype generation. | |
| --pruning-lod-threshold |
2.302585092994046 | Ln likelihood ratio threshold for adaptive pruning algorithm | |
| --pruning-seeding-lod-threshold |
9.210340371976184 | Ln likelihood ratio threshold for seeding subgraph of good variation in adaptive pruning algorithm | |
| --recover-all-dangling-branches |
false | Recover all dangling branches | |
| --reference-model-deletion-quality |
30 | The quality of deletion in the reference model | |
| --showHidden |
false | display hidden arguments | |
| --smith-waterman |
FASTEST_AVAILABLE | Which Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice | |
| --smith-waterman-dangling-end-gap-extend-penalty |
-6 | Smith-Waterman gap-extend penalty for dangling-end recovery. | |
| --smith-waterman-dangling-end-gap-open-penalty |
-110 | Smith-Waterman gap-open penalty for dangling-end recovery. | |
| --smith-waterman-dangling-end-match-value |
25 | Smith-Waterman match value for dangling-end recovery. | |
| --smith-waterman-dangling-end-mismatch-penalty |
-50 | Smith-Waterman mismatch penalty for dangling-end recovery. | |
| --smith-waterman-haplotype-to-reference-gap-extend-penalty |
-11 | Smith-Waterman gap-extend penalty for haplotype-to-reference alignment. | |
| --smith-waterman-haplotype-to-reference-gap-open-penalty |
-260 | Smith-Waterman gap-open penalty for haplotype-to-reference alignment. | |
| --smith-waterman-haplotype-to-reference-match-value |
200 | Smith-Waterman match value for haplotype-to-reference alignment. | |
| --smith-waterman-haplotype-to-reference-mismatch-penalty |
-150 | Smith-Waterman mismatch penalty for haplotype-to-reference alignment. | |
| --smith-waterman-read-to-haplotype-gap-extend-penalty |
-5 | Smith-Waterman gap-extend penalty for read-to-haplotype alignment. | |
| --smith-waterman-read-to-haplotype-gap-open-penalty |
-30 | Smith-Waterman gap-open penalty for read-to-haplotype alignment. | |
| --smith-waterman-read-to-haplotype-match-value |
10 | Smith-Waterman match value for read-to-haplotype alignment. | |
| --smith-waterman-read-to-haplotype-mismatch-penalty |
-15 | Smith-Waterman mismatch penalty for read-to-haplotype alignment. | |
| --soft-clip-low-quality-ends |
false | If enabled will preserve low-quality read ends as softclips (used for DRAGEN-GATK BQD genotyper model) | |
| --transform-dragen-mapping-quality |
false | If enabled this argument will map DRAGEN aligner aligned reads with mapping quality <=250 to scale up to MQ 50 | |
| --use-filtered-reads-for-annotations |
false | Use the contamination-filtered read maps for the purposes of annotating variants | |
| --use-pdhmm-overlap-optimization |
false | PDHMM: An optimization to PDHMM, if set this will skip running PDHMM haplotype determination on reads that don't overlap (within a few bases) of the determined allele in each haplotype. This substantially reduces the amount of read-haplotype comparisons at the expense of ignoring read realignment mapping artifacts. (Requires '--use-pdhmm' argument) | |
| Deprecated Arguments | |||
| --recover-dangling-heads |
false | (Deprecated) This argument is deprecated since version 3.3 | |
| --use-new-qual-calculator -new-qual |
true | (Deprecated) Use the new AF model instead of the so-called exact model | |
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
Minimum probability for a locus to be considered active.
double 0.002 [ [ -∞ ∞ ] ]
Use Mutect2's adaptive graph pruning algorithm
A single edge multiplicity cutoff for pruning doesn't work in samples with variable depths, for example exomes
and RNA. This parameter enables the probabilistic algorithm for pruning the assembly graph that considers the
likelihood that each chain in the graph comes from real variation.
boolean false
Initial base error rate estimate for adaptive pruning
Initial base error rate guess for the probabilistic adaptive pruning model. Results are not very sensitive to this
parameter because it is only a starting point from which the algorithm discovers the true error rate.
double 0.001 [ [ -∞ ∞ ] ]
If true, adds a command line header line to created VCF files.
boolean true
Annotate all sites with PLs
Advanced, experimental argument: if SNP likelihood model is specified, and if EMIT_ALL_ACTIVE_SITES output mode is set, when we set this argument then we will also emit PLs at all sites. This will give a measure of reference confidence and a measure of which alt alleles are more plausible (if any).
WARNINGS:
- This feature will inflate VCF file size considerably.
- All SNP ALT alleles will be emitted with corresponding 10 PL values.
- An error will be emitted if EMIT_ALL_ACTIVE_SITES is not set, or if anything other than diploid SNP model is used
boolean false
Likelihood and read-based annotations will only take into consideration reads that overlap the variant or any base no further than this distance expressed in base pairs
int 2 [ [ -∞ ∞ ] ]
The set of alleles to force-call regardless of evidence
FeatureInput[VariantContext] null
Allow graphs that have non-unique kmers in the reference
By default, the program does not allow processing of reference sections that contain non-unique kmers. Disabling
this check may cause problems in the assembly graph.
boolean false
If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site
Depending on the value of the --max_alternate_alleles argument, we may genotype only a fraction of the alleles being sent on for genotyping. Using this argument instructs the genotyper to annotate (in the INFO field) the number of alternate alleles that were originally discovered at the site.
boolean false
One or more specific annotations to add to variant calls
Which annotations to include in variant calls in the output. These supplement annotations provided by annotation groups.
List[String] []
One or more groups of annotations to apply to variant calls
Which groups of annotations to add to the output variant calls. Any requirements that are not met (e.g. failing to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.
List[String] []
One or more specific annotations to exclude from variant calls
Which annotations to exclude from output in the variant calls. Note that this argument has higher priority than the
-A or -G arguments, so these annotations will be excluded even if they are explicitly included with the other
options.
List[String] []
If enabled this argument will apply the DRAGEN-GATK BaseQualityDropout model to the genotyping model for filtering sites due to Linked Error mode.
boolean false
If enabled this argument will apply the DRAGEN-GATK ForeignReadDetection model to the genotyping model for filtering sites.
boolean false
read one or more arguments files and add them to the command line
List[File] []
Number of additional bases of context to include around each assembly region
Parameters that control assembly regions
int 100 [ [ -∞ ∞ ] ]
File to which assembled haplotypes should be written
The assembled haplotypes and locally realigned reads will be written as BAM to this file if requested. Really
for debugging purposes only. Note that the output here does not include uninformative reads so that not every
input read is emitted to the bam.
Turning on this mode may result in serious performance cost for the caller. It's really only appropriate to
use in specific areas where you want to better understand why the caller is making specific calls.
The reads are written out containing an "HC" tag (integer) that encodes which haplotype each read best matches
according to the haplotype caller's likelihood calculation. The use of this tag is primarily intended
to allow good coloring of reads in IGV. Simply go to "Color Alignments By > Tag" and enter "HC" to more
easily see which reads go with these haplotype.
Note that the haplotypes (called or all, depending on mode) are emitted as single reads covering the entire
active region, coming from sample "HC" and a special read group called "ArtificialHaplotype". This will increase the
pileup depth compared to what would be expected from the reads only, especially in complex regions.
Note also that only reads that are actually informative about the haplotypes are emitted. By informative we mean
that there's a meaningful difference in the likelihood of the read coming from one haplotype compared to
its next best haplotype.
If multiple BAMs are passed as input to the tool (as is common for M2), then they will be combined in the bamout
output and tagged with the appropriate sample names.
The best way to visualize the output of this mode is with IGV. Tell IGV to color the alignments by tag,
and give it the "HC" tag, so you can see which reads support each haplotype. Finally, you can tell IGV
to group by sample, which will separate the potential haplotypes from the reads. All of this can be seen in
https://www.dropbox.com/s/xvy7sbxpf13x5bp/haplotypecaller%20bamout%20for%20docs.png this screenshot
String null
maximum number of bytes to read from a file into each partition of reads. Setting this higher will result in fewer partitions. Note that this will not be equal to the size of the partition in memory. Defaults to 0, which uses the default split size (determined by the Hadoop input format, typically the size of one HDFS block).
long 0 [ [ -∞ ∞ ] ]
Which haplotypes should be written to the BAM
The type of BAM output we want to see. This determines whether HC will write out all of the haplotypes it
considered (top 128 max) or just the ones that were selected as alleles and assigned to samples.
The --bam-writer-type argument is an enumerated type (WriterType), which can have one of the following values:
WriterType CALLED_HAPLOTYPES
Base qualities below this threshold will be reduced to the minimum (6)
Bases with a quality below this threshold will reduced to the minimum usable qualiy score (6).
byte 18 [ [ -∞ ∞ ] ]
Comparison VCF file(s)
If a call overlaps with a record from the provided comp track, the INFO field will be annotated
as such in the output with the track name (e.g. -comp:FOO will have 'FOO' in the INFO field). Records that are
filtered in the comp track will be ignored. Note that 'dbSNP' has been special-cased (see the --dbsnp argument).
List[FeatureInput[VariantContext]] []
Spark properties to set on the Spark context in the format
List[String] []
Tab-separated File containing fraction of contamination in sequencing data (per sample) to aggressively remove. Format should be "
This argument specifies a file with two columns "sample" and "contamination" specifying the contamination level for those samples. Samples that do not appear in this file will be processed with CONTAMINATION_FRACTION.
File null
Fraction of contamination in sequencing data (for all samples) to aggressively remove
If this fraction is greater is than zero, the caller will aggressively attempt to remove contamination through biased down-sampling of reads. Basically, it will ignore the contamination fraction of reads for each alternate allele. So if the pileup contains N total bases, then we
will try to remove (N * contamination fraction) bases for each alternate allele.
double 0.0 [ [ -∞ ∞ ] ]
If true, create a BAM index when writing a coordinate-sorted BAM file.
boolean true
If true, create a BAM splitting index (SBI) when writing a coordinate-sorted BAM file.
boolean true
If true, create a VCF index when writing a coordinate-sorted VCF file.
boolean true
dbSNP file
A dbSNP VCF file.
FeatureInput[VariantContext] null
Print out verbose debug information about each assembly region
boolean false
If false this disables capping of base qualities in the HMM to the mapping quality of the read
boolean false
Don't skip calculations in ActiveRegions with no variants
If set, certain "early exit" optimizations in HaplotypeCaller, which aim to save compute and time by skipping
calculations if an ActiveRegion is determined to contain no variants, will be disabled. This is most likely to be useful if
you're using the -bamout argument to examine the placement of reads following reassembly and are interested in seeing the mapping of
reads in regions with no variations. Setting the --force-active flag may also be necessary.
boolean false
Read filters to be disabled before analysis
List[String] []
If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
boolean false
If enabled this argument will disable inclusion of the '*' spanning event when genotyping events that overlap deletions
boolean false
Toggle to revive legacy behavior of asymmetrically normalizing the arguments to the reference haplotype
boolean false
Disable all tool default annotations
Hook allowing for the user to remove default annotations from the tool
boolean false
Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
boolean false
Disable overlapping base quality correction
Base quality is capped at half of PCR error rate for bases where read and mate overlap, to account for full correlation of PCR errors at these bases. This argument disables that correction.
boolean false
Disable physical phasing
As of GATK 3.3, HaplotypeCaller outputs physical (read-based) information (see version 3.3 release notes and documentation for details). This argument disables that behavior.
boolean false
Disable iterating over kmer sizes when graph cycles are detected
When graph cycles are detected, the normal behavior is to increase kmer sizes iteratively until the cycles are
resolved. Disabling this behavior may cause the program to give up on assembling the ActiveRegion.
boolean false
disable DRAGstr pair-hmm score even when dragstr-params-path was provided
boolean false
Forfeit the use of the DRAGstr model to calculate genotype priors. This argument does not have any effect in the absence of DRAGstr model parameters (--dragstr-model-params)
boolean false
Do not analyze soft clipped bases in the reads
boolean false
Single argument for enabling the bulk of DRAGEN-GATK features including new developments for concordance against DRAGEN 3.7.8. NOTE: THIS WILL OVERWRITE PROVIDED ARGUMENT CHECK TOOL INFO TO SEE WHICH ARGUMENTS ARE SET).
DRAGEN-GATK version 2: This includes PDHMM and Columnwise detection (with hopes to add Joint Detection and new STRE as well in the future)
Exclusion: This argument cannot be used at the same time as dragen-mode.
Boolean false
Single argument for enabling the bulk of DRAGEN-GATK features. NOTE: THIS WILL OVERWRITE PROVIDED ARGUMENT CHECK TOOL INFO TO SEE WHICH ARGUMENTS ARE SET).
DRAGEN-GATK mode changes a long list of arguments to support running DRAGEN-GATK with FRD + BQD + STRE (with or without
a provided STRE table provided):
Exclusion: This argument cannot be used at the same time as dragen-378-concordance-mode.
Boolean false
het to hom prior ratio use with DRAGstr on
int 2 [ [ -∞ ∞ ] ]
location of the DRAGstr model parameters for STR error correction used in the Pair HMM. When provided, it overrides other PCR error correcting mechanisms
GATKPath null
Mode for emitting reference confidence scores (For Mutect2, this is a BETA feature)
The reference confidence mode makes it possible to emit a per-bp or summarized confidence estimate for a site being strictly homozygous-reference. See https://software.broadinstitute.org/gatk/documentation/article.php?id=4017 for information about GVCFs.
For Mutect2, this is a BETA feature that functions similarly to the HaplotypeCaller reference confidence/GVCF mode.
The --emit-ref-confidence argument is an enumerated type (ReferenceConfidenceMode), which can have one of the following values:
ReferenceConfidenceMode NONE
Use all possible annotations (not for the faint of heart)
You can use the -AX argument in combination with this one to exclude specific annotations. Note that some
annotations may not be actually applied if they are not applicable to the data provided or if they are
unavailable to the tool (e.g. there are several annotations that are currently not hooked up to
HaplotypeCaller). At present no error or warning message will be provided, the annotation will simply be
skipped silently. You can check the output VCF header to see which annotations were activated and thus might be applied (although
this does not guarantee that the annotation was applied to all records in the VCF, since some annotations have
additional requirements, e.g. minimum number of samples or heterozygous sites only -- see the documentation
for individual annotations' requirements).
boolean false
Will enable less strict read disqualification low base quality reads
If enabled, rather than disqualifying all reads over a threshold of minimum hmm scores we will instead choose a less strict
and less aggressive cap for disqualification based on the read length and base qualities.
boolean false
One or more genomic intervals to exclude from processing
Use this argument to exclude certain parts of the genome from the analysis (like -L, but the opposite). This argument can be specified multiple times. You can use samtools-style intervals either explicitly on the
command line (e.g. -XL 1 or -XL 1:100-200) or by loading in a file containing a list of intervals
(e.g. -XL myFile.intervals). strings gathered from the command line -XL argument to be parsed into intervals to exclude
List[String] []
Error rate used to set expectation for post HMM read disqualification based on mismatches
double 0.02 [ [ -∞ ∞ ] ]
Output the band lower bound for each GQ block regardless of the data it represents
Output the band lower bound for each GQ block instead of the min GQ -- for better compression
boolean false
Collapse long flow-based hmers only up to difference in reference
boolean false
Cap probabilities of error to 1 relative to base call
boolean false
Value to fill the zeros of the matrix with
double 0.001 [ [ -∞ ∞ ] ]
pre-filter alleles before genotyping
boolean false
Threshold for prefiltering alleles on quality
float 30.0 [ [ -∞ ∞ ] ]
Threshold for prefiltering alleles on SOR
float 3.0 [ [ -∞ ∞ ] ]
Remove also lone alleles during allele filtering
boolean false
Should all probabilities of insertion or deletion in the flow be combined together
boolean false
Modifications instructions to the read flow matrix. Format is src,dst{,src,dst}+. Example: 10,12,11,12 - these instructions will copy element 10 into 11 and 12
String null
Single argument for enabling the bulk of Flow Based features. NOTE: THIS WILL OVERWRITE PROVIDED ARGUMENT CHECK TOOL INFO TO SEE WHICH ARGUMENTS ARE SET).
The --flow-mode argument is an enumerated type (FlowMode), which can have one of the following values:
FlowMode NONE
flow order used for this annotations. [readGroup:]flowOrder
List[String] []
probability scaling factor for (phred=10) for probability quantization
int 10 [ [ -∞ ∞ ] ]
Number of bins for probability quantization
int 121 [ [ -∞ ∞ ] ]
Should the probabilities of more then 1 indel be used
boolean false
Remove probabilities of basecall of zero from non-zero genome
boolean false
Report either insertion or deletion, probability, not both
boolean false
Keep only hmer/2 probabilities (like in base format)
boolean false
Should indel probabilities be symmetric in flow
boolean false
Use t0 tag if exists in the read to create flow matrix
boolean false
If provided, all regions will be marked as active
boolean false
Force-call filtered alleles included in the resource specified by --alleles
boolean false
Samples representing the population "founders"
List[String] []
A configuration file to use with the GATK.
String null
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.
String ""
How we assign genotypes
The --genotype-assignment-method argument is an enumerated type (GenotypeAssignmentMethod), which can have one of the following values:
GenotypeAssignmentMethod USE_PLS_TO_ASSIGN
Write debug assembly graph information to this file
This argument is meant for debugging and is not immediately useful for normal analysis use.
String null
Exclusive upper bounds for reference confidence GQ bands (must be in [1, 100] and specified in increasing order)
When HC is run in reference confidence mode with banding compression enabled (-ERC GVCF), homozygous-reference
sites are compressed into bands of similar genotype quality (GQ) that are emitted as a single VCF record. See
the FAQ documentation for more details about the GVCF format.
This argument allows you to set the GQ bands. HC expects a list of strictly increasing GQ values
that will act as exclusive upper bounds for the GQ bands. To pass multiple values,
you provide them one by one with the argument, as in `-GQB 10 -GQB 20 -GQB 30` and so on
(this would set the GQ bands to be `[0, 10), [10, 20), [20, 30)` and so on, for example).
Note that GQ values are capped at 99 in the GATK, so values must be integers in [1, 100].
If the last value is strictly less than 100, the last GQ band will start at that value (inclusive)
and end at 100 (exclusive).
List[Integer] [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99]
display the help message
boolean false
Heterozygosity value used to compute prior probabilities for any locus. See the GATKDocs for full details on the meaning of this population genetics concept
The expected heterozygosity value used to compute prior probability that a locus is non-reference. The default priors are for provided for humans:
het = 1e-3
which means that the probability of N samples being hom-ref at a site is:
1 - sum_i_2N (het / i)
Note that heterozygosity as used here is the population genetics concept:
http://en.wikipedia.org/wiki/Zygosity#Heterozygosity_in_population_genetics
That is, a hets value of 0.01 implies that two randomly chosen chromosomes from the population of organisms
would differ from each other (one being A and the other B) at a rate of 1 in 100 bp.
Note that this quantity has nothing to do with the likelihood of any given sample having a heterozygous genotype,
which in the GATK is purely determined by the probability of the observed data P(D | AB) under the model that there
may be a AB het genotype. The posterior probability of this AB genotype would use the het prior, but the GATK
only uses this posterior probability in determining the prob. that a site is polymorphic. So changing the
het parameters only increases the chance that a site will be called non-reference across all samples, but
doesn't actually change the output genotype likelihoods at all, as these aren't posterior probabilities at all.
The quantity that changes whether the GATK considers the possibility of a het genotype at all is the ploidy,
which determines how many chromosomes each individual in the species carries.
Double 0.001 [ [ -∞ ∞ ] ]
Standard deviation of heterozygosity for SNP and indel calling.
The standard deviation of the distribution of alt allele fractions. The above heterozygosity parameters give the
*mean* of this distribution; this parameter gives its spread.
double 0.01 [ [ -∞ ∞ ] ]
Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept
This argument informs the prior probability of having an indel at a site.
double 1.25E-4 [ [ -∞ ∞ ] ]
The size of an indel to check for in the reference model
This parameter determines the maximum size of an indel considered as potentially segregating in the
reference model. It is used to eliminate reads from being indel informative at a site, and determines
by that mechanism the certainty in the reference base. Conceptually, setting this parameter to
X means that each informative read is consistent with any indel of size X being present at a specific
position in the genome, given its alignment to the reference.
int 10 [ [ -∞ ∞ ] ]
BAM/SAM/CRAM file containing reads
R List[GATKPath] []
Amount of padding (in bp) to add to each interval you are excluding.
Use this to add padding to the intervals specified using -XL. For example, '-XL 1:100' with a
padding value of 20 would turn into '-XL 1:80-120'. This is typically used to add padding around targets when
analyzing exomes.
int 0 [ [ -∞ ∞ ] ]
Interval merging rule for abutting intervals
By default, the program merges abutting intervals (i.e. intervals that are directly side-by-side but do not
actually overlap) into a single continuous interval. However you can change this behavior if you want them to be
treated as separate intervals instead.
The --interval-merging-rule argument is an enumerated type (IntervalMergingRule), which can have one of the following values:
IntervalMergingRule ALL
Amount of padding (in bp) to add to each interval you are including.
Use this to add padding to the intervals specified using -L. For example, '-L 1:100' with a
padding value of 20 would turn into '-L 1:80-120'. This is typically used to add padding around targets when
analyzing exomes.
int 0 [ [ -∞ ∞ ] ]
Set merging approach to use for combining interval inputs
By default, the program will take the UNION of all intervals specified using -L and/or -XL. However, you can
change this setting for -L, for example if you want to take the INTERSECTION of the sets instead. E.g. to
perform the analysis only on chromosome 1 exomes, you could specify -L exomes.intervals -L 1 --interval-set-rule
INTERSECTION. However, it is not possible to modify the merging approach for intervals passed using -XL (they will
always be merged using UNION).
Note that if you specify both -L and -XL, the -XL interval set will be subtracted from the -L interval set.
The --interval-set-rule argument is an enumerated type (IntervalSetRule), which can have one of the following values:
IntervalSetRule UNION
One or more genomic intervals over which to operate
List[String] []
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters).
List[String] []
prevent spreading of boundary flows.
boolean false
Kmer size to use in the read threading assembler
Multiple kmer sizes can be specified, using e.g. `--kmer-size 10 --kmer-size 25`.
List[Integer] [10, 25]
What likelihood calculation engine to use to calculate the relative likelihood of reads vs haplotypes
The --likelihood-calculation-engine argument is an enumerated type (Implementation), which can have one of the following values:
Implementation PairHMM
If enabled, the Assembly Engine will construct a Linked De Bruijn graph to recover better haplotypes
Disables graph simplification into a seq graph, opts to construct a proper De Bruijn graph with potential loops
NOTE: --linked-de-bruijn-graph is currently an experimental feature that does not directly match with
the regular HaplotypeCaller. Specifically the haplotype finding code does not perform correctly at complicated
sites. Use this mode at your own risk.
boolean false
Control the threshold for discounting reads from the genotyper due to mapping quality after the active region detection and assembly steps but before genotyping. NOTE: this is in contrast to the --minimum-mapping-quality argument which filters reads from all parts of the HaplotypeCaller. If you would like to call genotypes with a different threshold both arguments must be set.
int 20 [ [ -∞ ∞ ] ]
Maximum number of alternate alleles to genotype
If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES),
then only this many alleles will be used. Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it
scales exponentially based on the number of alternate alleles.
Unless there is a good reason to change the default value, we highly recommend
that you not play around with this parameter.
See also and .
This value can be no greater than one less than the corresponding GenomicsDB argument. Sites that exceed the
GenomicsDB alt allele max will not be output with likelihoods and will be dropped by GenotypeGVCFs.
int 6 [ [ -∞ ∞ ] ]
Maximum size of an assembly region
int 300 [ [ -∞ ∞ ] ]
Set the maximum depth to modify FRD adjustment to in the event of high depth sites (0 to disable)
int 0 [ [ -∞ ∞ ] ]
Maximum number of genotypes to consider at any site
If there are more than this number of genotypes at a locus presented to the genotyper, then only this many genotypes will be used. The possible genotypes are simply different ways of partitioning alleles given a specific ploidy assumption.
Therefore, we remove genotypes from consideration by removing alternate alleles that are the least well supported.
The estimate of allele support is based on the ranking of the candidate haplotypes coming out of the graph building step.
Note that the reference allele is always kept.
Note that genotyping sites with large genotype counts is both CPU and memory intensive.
Unless there is a good reason to change the default value, we highly recommend that you not play around with this parameter.
The maximum number of alternative alleles used in the genotyping step will be the lesser of the two:
1. the largest number of alt alleles, given ploidy, that yields a genotype count no higher than
2. the value of
See also and
int 1024 [ [ -∞ ∞ ] ]
Two or more phased substitutions separated by this distance or less are merged into MNPs.
Two or more phased substitutions separated by this distance or less are merged into MNPs.
int 0 [ [ -∞ ∞ ] ]
Maximum number of haplotypes to consider for your population
The assembly graph can be quite complex, and could imply a very large number of possible haplotypes. Each haplotype
considered requires N PairHMM evaluations if there are N reads across all samples. In order to control the
run of the haplotype caller we only take maxNumHaplotypesInPopulation paths from the graph, in order of their
weights, no matter how many paths are possible to generate from the graph. Putting this number too low
will result in dropping true variation because paths that include the real variant are not even considered.
You can consider increasing this number when calling organisms with high heterozygosity.
int 128 [ [ -∞ ∞ ] ]
Upper limit on how many bases away probability mass can be moved around when calculating the boundaries between active and inactive assembly regions
int 50 [ [ -∞ ∞ ] ]
Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to 0 to disable.
Other parameters
int 50 [ [ -∞ ∞ ] ]
Maximum number of variants in graph the adaptive pruner will allow
The maximum number of variants in graph the adaptive pruner will allow
int 100 [ [ -∞ ∞ ] ]
Minimum size of an assembly region
Parameters that control active regions
int 50 [ [ -∞ ∞ ] ]
Minimum base quality required to consider a base for calling
Bases with a quality below this threshold will not be used for calling.
byte 10 [ [ -∞ ∞ ] ]
Minimum length of a dangling branch to attempt recovery
When constructing the assembly graph we are often left with "dangling" branches. The assembly engine attempts to rescue these branches
by merging them back into the main graph. This argument describes the minimum length of a dangling branch needed for the engine to
try to rescue it. A smaller number here will lead to higher sensitivity to real variation but also to a higher number of false positives.
int 4 [ [ -∞ ∞ ] ]
Minimum support to not prune paths in the graph
Paths with fewer supporting kmers than the specified threshold will be pruned from the graph. Be aware that this argument can dramatically affect the results of variant calling and should only be used with great caution.
Using a prune factor of 1 (or below) will prevent any pruning from the graph, which is generally not ideal; it can make the
calling much slower and even less accurate (because it can prevent effective merging of "tails" in the graph). Higher values
tend to make the calling much faster, but also lowers the sensitivity of the results (because it ultimately requires higher
depth to produce calls).
int 2 [ [ -∞ ∞ ] ]
How many threads should a native pairHMM implementation use
int 4 [ [ -∞ ∞ ] ]
use double precision in the native pairHmm. This is slower but matches the java implementation better
boolean false
Number of samples that must pass the minPruning threshold
If fewer samples than the specified number pass the minPruning threshold for a given path, that path will be eliminated from the graph.
int 1 [ [ -∞ ∞ ] ]
For tools that shuffle data or write an output, sets the number of reducers. Defaults to 0, which gives one partition per 10MB of input.
int 0 [ [ -∞ ∞ ] ]
Number of hom-ref genotypes to infer at sites not present in a panel
When a variant is not seen in any panel, this argument controls whether to infer (and with what effective strength)
that only reference alleles were observed at that site. E.g. "If not seen in 1000Genomes, treat it as AC=0,
AN=2000".
int 0 [ [ -∞ ∞ ] ]
Single file to which variants should be written
R String null
Specifies which type of calls we should output
The --output-mode argument is an enumerated type (OutputMode), which can have one of the following values:
OutputMode EMIT_VARIANTS_ONLY
when writing a bam, in single sharded mode this directory to write the temporary intermediate output shards, if not specified .parts/ will be used
Exclusion: This argument cannot be used at the same time as sharded-output.
String null
Flat gap continuation penalty for use in the Pair HMM
int 10 [ [ -∞ ∞ ] ]
The PairHMM implementation to use for genotype likelihood calculations
The PairHMM implementation to use for genotype likelihood calculations. The various implementations balance a tradeoff of accuracy and runtime.
The --pair-hmm-implementation argument is an enumerated type (Implementation), which can have one of the following values:
Implementation FASTEST_AVAILABLE
File to write exact pairHMM inputs/outputs to for debugging purposes
Argument for generating a file of all of the inputs and outputs for the pair hmm
GATKPath null
The PCR indel model to use
When calculating the likelihood of variants, we can try to correct for PCR errors that cause indel artifacts. The correction is based on the reference context, and acts specifically around repetitive sequences that tend
to cause PCR errors). The variant likelihoods are penalized in increasing scale as the context around a
putative indel is more repetitive (e.g. long homopolymer). The correction can be disabling by specifying
'-pcrModel NONE'; in that case the default base insertion/deletion qualities will be used (or taken from the
read if generated through the BaseRecalibrator). VERY IMPORTANT: when using PCR-free sequencing data we
definitely recommend setting this argument to NONE .
The --pcr-indel-model argument is an enumerated type (PCRErrorModel), which can have one of the following values:
PCRErrorModel CONSERVATIVE
Pedigree file for determining the population "founders"
GATKPath null
The global assumed mismapping rate for reads
The phredScaledGlobalReadMismappingRate reflects the average global mismapping rate of all reads, regardless of their
mapping quality. This term effects the probability that a read originated from the reference haplotype, regardless of
its edit distance from the reference, in that the read could have originated from the reference haplotype but
from another location in the genome. Suppose a read has many mismatches from the reference, say like 5, but
has a very high mapping quality of 60. Without this parameter, the read would contribute 5 * Q30 evidence
in favor of its 5 mismatch haplotype compared to reference, potentially enough to make a call off that single
read for all of these events. With this parameter set to Q30, though, the maximum evidence against any haplotype
that this (and any) read could contribute is Q30.
Set this term to any negative number to turn off the global mapping rate.
int 45 [ [ -∞ ∞ ] ]
If enabled, the variant caller will create pileup-based haplotypes in addition to the assembly-based haplotype generation.
Enables pileup-based haplotype creation and variant detection
NOTE: --pileup-detection is a beta feature. Use this mode at your own risk.
boolean false
Interval file with column specifying desired ploidy for genotyping models. Overrides default ploidy and user-provided --ploidy argument in specific regions.
FeatureInput[NamedFeature] null
Callset to use in calculating genotype priors
Supporting external panel. Allele counts from this panel (taken from AC,AN or MLEAC,AN or raw genotypes) will
be used to inform the frequency distribution underlying the genotype priors. These files must be VCF 4.2 spec or later.
Note that unlike CalculateGenotypePosteriors, HaplotypeCaller only allows one supporting callset.
FeatureInput[VariantContext] null
Name of the program running
String null
Ln likelihood ratio threshold for adaptive pruning algorithm
Log-10 likelihood ratio threshold for adaptive pruning algorithm.
double 2.302585092994046 [ [ -∞ ∞ ] ]
Ln likelihood ratio threshold for seeding subgraph of good variation in adaptive pruning algorithm
Log-10 likelihood ratio threshold for adaptive pruning algorithm.
double 9.210340371976184 [ [ -∞ ∞ ] ]
Whether to suppress job-summary info on System.err.
Boolean false
Read filters to be applied before analysis
List[String] []
Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.
List[GATKPath] []
Each read shard has this many bases of extra context on each side. Read shards must have as much or more padding than assembly regions.
int 100 [ [ -∞ ∞ ] ]
Maximum size of each read shard, in bases. For good performance, this should be much larger than the maximum assembly region size.
int 5000 [ [ -∞ ∞ ] ]
Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
The --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:
ValidationStringency SILENT
Recover all dangling branches
By default, the read threading assembler does not recover dangling branches that fork after splitting from the reference. This argument
tells the assembly engine to recover all dangling branches.
boolean false
(Deprecated)
This argument is deprecated since version 3.3
As of version 3.3, this argument is no longer needed because dangling end recovery is now the default behavior. See GATK 3.3 release notes for more details.
boolean false
Reference sequence file
R GATKPath null
The quality of deletion in the reference model
This parameter is determining the deletion quality in the reference confidence model.
byte 30 [ [ -∞ ∞ ] ]
Name of single sample to use from a multi-sample bam
You can use this argument to specify that HC should process a single sample out of a multisample BAM file. This
is especially useful if your samples are all in the same file but you need to run them individually through HC
in -ERC GVC mode (which is the recommended usage). Note that the name is case-sensitive.
String null
Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).
Sample ploidy - equivalent to number of chromoso
mes per pool. In pooled experiments this should be = # of samples in pool * individual sample ploidy
int 2 [ [ -∞ ∞ ] ]
For tools that write an output, write the output in multiple pieces (shards)
Exclusion: This argument cannot be used at the same time as output-shard-tmp-dir.
boolean false
display hidden arguments
boolean false
whether to use the shuffle implementation or not
boolean false
Which Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice
The --smith-waterman argument is an enumerated type (Implementation), which can have one of the following values:
Implementation FASTEST_AVAILABLE
Smith-Waterman gap-extend penalty for dangling-end recovery.
int -6 [ [ -∞ 0 ] ]
Smith-Waterman gap-open penalty for dangling-end recovery.
int -110 [ [ -∞ 0 ] ]
Smith-Waterman match value for dangling-end recovery.
int 25 [ [ 0 ∞ ] ]
Smith-Waterman mismatch penalty for dangling-end recovery.
int -50 [ [ -∞ 0 ] ]
Smith-Waterman gap-extend penalty for haplotype-to-reference alignment.
int -11 [ [ -∞ 0 ] ]
Smith-Waterman gap-open penalty for haplotype-to-reference alignment.
int -260 [ [ -∞ 0 ] ]
Smith-Waterman match value for haplotype-to-reference alignment.
int 200 [ [ 0 ∞ ] ]
Smith-Waterman mismatch penalty for haplotype-to-reference alignment.
int -150 [ [ -∞ 0 ] ]
Smith-Waterman gap-extend penalty for read-to-haplotype alignment.
int -5 [ [ -∞ 0 ] ]
Smith-Waterman gap-open penalty for read-to-haplotype alignment.
int -30 [ [ -∞ 0 ] ]
Smith-Waterman match value for read-to-haplotype alignment.
int 10 [ [ 0 ∞ ] ]
Smith-Waterman mismatch penalty for read-to-haplotype alignment.
int -15 [ [ -∞ 0 ] ]
If enabled will preserve low-quality read ends as softclips (used for DRAGEN-GATK BQD genotyper model)
boolean false
URL of the Spark Master to submit jobs to when using the Spark pipeline runner.
String local[*]
Spark verbosity. Overrides --verbosity for Spark-generated logs only. Possible values: {ALL, DEBUG, INFO, WARN, ERROR, FATAL, OFF, TRACE}
String null
Granularity to use when writing a splitting index, one entry will be put into the index every n reads where n is this granularity value. Smaller granularity results in a larger index with more available split points.
long 4096 [ [ 1 ∞ ] ]
The minimum phred-scaled confidence threshold at which variants should be called
The minimum phred-scaled confidence threshold at which variants should be called. Only variant sites with QUAL equal
or greater than this threshold will be called. Note that since version 3.7, we no longer differentiate high confidence
from low confidence calls at the calling step. The default call confidence threshold is set low intentionally to achieve
high sensitivity, which will allow false positive calls as a side effect. Be sure to perform some kind of filtering after
calling to reduce the amount of false positives in your final callset. Note that when HaplotypeCaller is used in GVCF mode
(using either -ERC GVCF or -ERC BP_RESOLUTION) the call threshold is automatically set to zero. Call confidence thresholding
will then be performed in the subsequent GenotypeGVCFs command.
Note that the default was changed from 10.0 to 30.0 in version 4.1.0.0 to accompany the switch to use the the new quality score by default.
double 30.0 [ [ -∞ ∞ ] ]
whether to use the strict implementation or not (defaults to the faster implementation that doesn't strictly match the walker version)
boolean false
Temp directory to use.
GATKPath null
If enabled this argument will map DRAGEN aligner aligned reads with mapping quality <=250 to scale up to MQ 50
boolean false
Use the contamination-filtered read maps for the purposes of annotating variants
boolean false
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
(Deprecated)
Use the new AF model instead of the so-called exact model
As of version 4.1.0.0, this argument is no longer needed because the new qual score is now on by default. See GATK 3.3 release notes for more details.
boolean true
Whether to use NIO or the Hadoop filesystem (default) for reading files. (Note that the Hadoop filesystem is always used for writing files.)
boolean false
Partially Determined HMM, an alternative to the regular assembly haplotypes where we instead construct artificial haplotypes out of the union of the assembly and pileup alleles.
This argument enables the PartiallyDeterminedHMM. By enabling this triggers the HaplotypeCaller (not currently supported in Mutect2) to use the PDHMM to compute likelihoods instead of the PairHMM.
This means that variants found by both pileupdetection and the assembly engine are going to be treated as equivalent and merged/filtered together
to produce "PartiallyDetermined" Haplotype objects and produce a merged likelihoods score from multiple haplotypes being run together.
This code is intended for Dragen 3.7.8 concordance and is not recommended to be run outside of that context without being optimized.
boolean false
PDHMM: An optimization to PDHMM, if set this will skip running PDHMM haplotype determination on reads that don't overlap (within a few bases) of the determined allele in each haplotype. This substantially reduces the amount of read-haplotype comparisons at the expense of ignoring read realignment mapping artifacts. (Requires '--use-pdhmm' argument)
boolean false
if available, use the genotype posterior probabilities to calculate the site QUAL
boolean false
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
LogLevel INFO
display the version number for this tool
boolean false
See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum
GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.