Produces readxhaplotype matrix with likelihoods of read / haplotype
gatk FlowPairHMMAlignReadsToHaplotypes \
-H ~{haplotype_list} -O ~{base_file_name}.matches.tsv \
-I ~{input_bam} --flow-use-t0-tag -E FBA \
--flow-fill-empty-bins-value 0.00001 --flow-probability-threshold 0.00001 \
--flow-likelihood-optimized-comp
{@GATK.walkertype ReadWalker}
This Read Filter is automatically applied to the data by the Engine before processing by FlowPairHMMAlignReadsToHaplotypes.
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 | |||
| --haplotypes -H |
Fasta file with haplotypes | ||
| --input -I |
BAM/SAM/CRAM file containing reads | ||
| --output -O |
Read x haplotype log-likelihood matrix | ||
| Optional Tool Arguments | |||
| --aligner -E |
FlowBased | Aligner: FlowBasedHMM or FlowBasedAligner (FlowBased) | |
| --arguments_file |
read one or more arguments files and add them to the command line | ||
| --base-quality-score-threshold |
18 | Base qualities below this threshold will be reduced to the minimum (6) | |
| --cloud-index-prefetch-buffer -CIPB |
-1 | Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset. | |
| --cloud-prefetch-buffer -CPB |
40 | Size of the cloud-only prefetch buffer (in MB; 0 to disable). | |
| --concise-output-format |
false | concise or expanded output format: expanded - output full read x haplotype, concise - output for each read best haplotype and score differences from the next best and the reference haplotype, default: false (expanded format) | |
| --disable-bam-index-caching -DBIC |
false | If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified. | |
| --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 | |
| --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 | |
| --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. | ||
| --help -h |
false | display the help message | |
| --interval-merging-rule -imr |
ALL | Interval merging rule for abutting intervals | |
| --intervals -L |
One or more genomic intervals over which to operate | ||
| --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 | |
| --ref-haplotype |
Fasta file with haplotypes | ||
| --reference -R |
Reference sequence | ||
| --sites-only-vcf-output |
false | If true, don't emit genotype fields when writing vcf file output. | |
| --version |
false | display the version number for this tool | |
| Optional Common Arguments | |||
| --add-output-sam-program-record |
true | If true, adds a PG tag to created SAM/BAM/CRAM files. | |
| --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/CRAM index when writing a coordinate-sorted BAM/CRAM file. | |
| --create-output-bam-md5 -OBM |
false | If true, create a MD5 digest for any BAM/SAM/CRAM file created | |
| --create-output-variant-index -OVI |
true | If true, create a VCF index when writing a coordinate-sorted VCF file. | |
| --create-output-variant-md5 -OVM |
false | If true, create a a MD5 digest any VCF file created. | |
| --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). | ||
| --lenient -LE |
false | Lenient processing of VCF files | |
| --max-variants-per-shard |
0 | If non-zero, partitions VCF output into shards, each containing up to the given number of records. | |
| --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. | |
| --seconds-between-progress-updates |
10.0 | Output traversal statistics every time this many seconds elapse | |
| --sequence-dictionary |
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file. | ||
| --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 | |||
| --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-symmetric-hmm-normalizing |
false | Toggle to revive legacy behavior of asymmetrically normalizing the arguments to the reference haplotype | |
| --expected-mismatch-rate-for-read-disqualification |
0.02 | Error rate used to set expectation for post HMM read disqualification based on mismatches | |
| --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-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-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 | |
| --keep-boundary-flows |
false | prevent spreading of boundary flows. | |
| --likelihood-calculation-engine |
PairHMM | What likelihood calculation engine to use to calculate the relative likelihood of reads vs haplotypes | |
| --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 | |
| --showHidden |
false | display hidden arguments | |
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.
If true, adds a PG tag to created SAM/BAM/CRAM files.
boolean true
If true, adds a command line header line to created VCF files.
boolean true
Aligner: FlowBasedHMM or FlowBasedAligner (FlowBased)
The --aligner argument is an enumerated type (Implementation), which can have one of the following values:
Implementation FlowBased
read one or more arguments files and add them to the command line
List[File] []
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 [ [ -∞ ∞ ] ]
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
int -1 [ [ -∞ ∞ ] ]
Size of the cloud-only prefetch buffer (in MB; 0 to disable).
int 40 [ [ -∞ ∞ ] ]
concise or expanded output format: expanded - output full read x haplotype, concise - output for each read best haplotype and score differences from the next best and the reference haplotype, default: false (expanded format)
boolean false
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
boolean true
If true, create a MD5 digest for any BAM/SAM/CRAM file created
boolean false
If true, create a VCF index when writing a coordinate-sorted VCF file.
boolean true
If true, create a a MD5 digest any VCF file created.
boolean false
If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.
boolean false
If false this disables capping of base qualities in the HMM to the mapping quality of the read
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
Toggle to revive legacy behavior of asymmetrically normalizing the arguments to the reference haplotype
boolean false
Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
boolean false
disable DRAGstr pair-hmm score even when dragstr-params-path was provided
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
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 [ [ -∞ ∞ ] ]
Cap probabilities of error to 1 relative to base call
boolean false
Value to fill the zeros of the matrix with
double 0.001 [ [ -∞ ∞ ] ]
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
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
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 ""
Fasta file with haplotypes
R GATKPath null
display the help message
boolean false
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
Lenient processing of VCF files
boolean false
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 non-zero, partitions VCF output into shards, each containing up to the given number of records.
int 0 [ [ 0 ∞ ] ]
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
Read x haplotype log-likelihood matrix
R 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
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 [ [ -∞ ∞ ] ]
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] []
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
Fasta file with haplotypes
String null
Reference sequence
GATKPath null
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
GATKPath null
display hidden arguments
boolean false
If true, don't emit genotype fields when writing vcf file output.
boolean false
Temp directory to use.
GATKPath null
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
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
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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.