CalibrateDragstrModel

estimates the parameters for the DRAGstr model

Category Short Variant Discovery

Overview

Estimates the parameters for the DRAGstr model for an input sample.

This tools takes in the sampling sites generated by {@link ComposeSTRTableFile} on the same reference as the input sample.

The end result is a text file containing three parameter tables (GOP, GCP, API) that can be fed directly to {@link HaplotypeCaller} --dragstr-params-path.

Additional Information

Read filters

This Read Filter is automatically applied to the data by the Engine before processing by CalibrateDragstrModel.

WellformedReadFilter

CalibrateDragstrModel specific arguments

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		where to write the parameter output file.
--reference -R		Reference sequence file
--str-table-path -str		location of the zip that contains the sampling sites for the reference
Optional Tool Arguments
--api-mono-threshold	3	Maximum drop allowed in the API parameter within a period between consecutive repeat length values in Phred scale
--api-values	0:1.0:40	Possible prior probabilities for the heterozygous indel call for the DRAGstr model parameter esimation. These are expressed in Phred scaled values with the following format: start:step:end. For example the default '10:1.0:50' indicate the sequence starting at 10 finishing at 50 sampled at 1.0 intervals.
--arguments_file		read one or more arguments files and add them to the command line
--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).
--debug-sites-output		table with information gather on the samples sites. Includes what sites were downsampled, disqualified or accepted for parameter estimation
--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!
--down-sample-size	4096	Targeted maximum number of cases per combination period repeat count, the larger the more precise but also the slower estimation.
--force-estimation	false	for testing purpose only; force parameter estimation even with few datapoints available
--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.
--gop-values	10:.25:50	Possible values for the gop parmeterThese are expressed in Phred scaled values with the following format: start:step:end. For example the default '10:1.0:50' indicate the sequence starting at 10 finishing at 50 sampled at 1.0 intervals.
--gp-values	10:1.0:50	Possible Gap-Penalty values for the DRAGstr model parameter esimation. These are expressed in Phred scaled values with the following format: start:step:end. For example the default '10:1.0:50' indicate the sequence starting at 10 finishing at 50 sampled at 1.0 intervals.
--help -h	false	display the help message
--het-to-hom-ratio	2.0	Possible prior probabilities for the heterozygous indel call for the DRAGstr model parameter esimation. These are expressed in Phred scaled values with the following format: start:step:end. For example the default '10:1.0:50' indicate the sequence starting at 10 finishing at 50 sampled at 1.0 intervals.
--interval-merging-rule -imr	ALL	Interval merging rule for abutting intervals
--intervals -L		One or more genomic intervals over which to operate
--max-period	8	maximum period considered in STR analysis
--max-repeats	20	maximum repeat length (in repeated units) considered in STR analyses
--min-loci-count	50	Minimum number of sites for a repeat count and period length pair. The estimation will combine pairs that have a smaller number of such cases (same period but +/- 1 repeat count)
--minimum-depth -md	10	Minimum coverage to consider a locus for sampling
--parallel	false	run alignment data collection and estimation in parallel
--pileup-padding	5	bases on either side of the repeat that are included in the STR pileup
--sampling-min-mq	20	the minimum read mapping quality allowed in sampled loci. Any read with a lower MQ will result in discarding that locus
--shard-size	1000000	when running in parallel this is the suggested shard size in base pairs. The actual shard-size may vary to adapt to small contigs and the requested number of threads
--sites-only-vcf-output	false	If true, don't emit genotype fields when writing vcf file output.
--threads	0	suggested number of parallel threads to perform the estimation, the default 0 leave it up to the VM to decide. When set to more than 1, this will activate parallel in the absence of --parallel
--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
--showHidden	false	display hidden arguments

Argument details

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.

--add-output-sam-program-record / -add-output-sam-program-record

If true, adds a PG tag to created SAM/BAM/CRAM files.

boolean true

--add-output-vcf-command-line / -add-output-vcf-command-line

If true, adds a command line header line to created VCF files.

boolean true

--api-mono-threshold

Maximum drop allowed in the API parameter within a period between consecutive repeat length values in Phred scale

int 3 [ [ 0 ∞ ] ]

--api-values

Possible prior probabilities for the heterozygous indel call for the DRAGstr model parameter esimation. These are expressed in Phred scaled values with the following format: start:step:end. For example the default '10:1.0:50' indicate the sequence starting at 10 finishing at 50 sampled at 1.0 intervals.

DoubleSequence 0:1.0:40

--arguments_file

read one or more arguments files and add them to the command line

List[File] []

--cloud-index-prefetch-buffer / -CIPB

Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.

int -1 [ [ -∞ ∞ ] ]

--cloud-prefetch-buffer / -CPB

Size of the cloud-only prefetch buffer (in MB; 0 to disable).

int 40 [ [ -∞ ∞ ] ]

--create-output-bam-index / -OBI

If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.

boolean true

--create-output-bam-md5 / -OBM

If true, create a MD5 digest for any BAM/SAM/CRAM file created

boolean false

--create-output-variant-index / -OVI

If true, create a VCF index when writing a coordinate-sorted VCF file.

boolean true

--create-output-variant-md5 / -OVM

If true, create a a MD5 digest any VCF file created.

boolean false

--debug-sites-output

table with information gather on the samples sites. Includes what sites were downsampled, disqualified or accepted for parameter estimation

String null

--disable-bam-index-caching / -DBIC

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

--disable-read-filter / -DF

Read filters to be disabled before analysis

List[String] []

--disable-sequence-dictionary-validation / -disable-sequence-dictionary-validation

If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!

boolean false

--disable-tool-default-read-filters / -disable-tool-default-read-filters

Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)

boolean false

--down-sample-size

Targeted maximum number of cases per combination period repeat count, the larger the more precise but also the slower estimation.

int 4096 [ [ 512 ∞ ] ]

--exclude-intervals / -XL

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] []

--force-estimation

for testing purpose only; force parameter estimation even with few datapoints available

boolean false

--gatk-config-file

A configuration file to use with the GATK.

String null

--gcs-max-retries / -gcs-retries

If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection

int 20 [ [ -∞ ∞ ] ]

--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.

String ""

--gop-values

Possible values for the gop parmeterThese are expressed in Phred scaled values with the following format: start:step:end. For example the default '10:1.0:50' indicate the sequence starting at 10 finishing at 50 sampled at 1.0 intervals.

DoubleSequence 10:.25:50

--gp-values

Possible Gap-Penalty values for the DRAGstr model parameter esimation. These are expressed in Phred scaled values with the following format: start:step:end. For example the default '10:1.0:50' indicate the sequence starting at 10 finishing at 50 sampled at 1.0 intervals.

DoubleSequence 10:1.0:50

--help / -h

display the help message

boolean false

--het-to-hom-ratio

double 2.0 [ [ 0 179,769,313,486,231,570,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000 ] ]

--input / -I

BAM/SAM/CRAM file containing reads

R List[GATKPath] []

--interval-exclusion-padding / -ixp

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 / -imr

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:

ALL
OVERLAPPING_ONLY

IntervalMergingRule ALL

--interval-padding / -ip

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 [ [ -∞ ∞ ] ]

--interval-set-rule / -isr

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:

UNION: Take the union of all intervals
INTERSECTION: Take the intersection of intervals (the subset that overlaps all intervals specified)

IntervalSetRule UNION

--intervals / -L

One or more genomic intervals over which to operate

List[String] []

--inverted-read-filter / -XRF

Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters).

List[String] []

--lenient / -LE

Lenient processing of VCF files

boolean false

--max-period

maximum period considered in STR analysis

int 8 [ [ 2 10 ] ]

--max-repeats

maximum repeat length (in repeated units) considered in STR analyses

int 20 [ [ 2 100 ] ]

--max-variants-per-shard

If non-zero, partitions VCF output into shards, each containing up to the given number of records.

int 0 [ [ 0 ∞ ] ]

--min-loci-count

Minimum number of sites for a repeat count and period length pair. The estimation will combine pairs that have a smaller number of such cases (same period but +/- 1 repeat count)

int 50 [ [ 1 ∞ ] ]

--minimum-depth / -md

Minimum coverage to consider a locus for sampling

int 10 [ [ -∞ ∞ ] ]

--output / -O

where to write the parameter output file.

R GATKPath null

--parallel

run alignment data collection and estimation in parallel

boolean false

--pileup-padding

bases on either side of the repeat that are included in the STR pileup

int 5 [ [ -∞ ∞ ] ]

--QUIET

Whether to suppress job-summary info on System.err.

Boolean false

--read-filter / -RF

Read filters to be applied before analysis

List[String] []

--read-index / -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.

List[GATKPath] []

--read-validation-stringency / -VS

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:

STRICT
LENIENT
SILENT

ValidationStringency SILENT

--reference / -R

Reference sequence file

R GATKPath null

--sampling-min-mq

the minimum read mapping quality allowed in sampled loci. Any read with a lower MQ will result in discarding that locus

int 20 [ [ -∞ ∞ ] ]

--seconds-between-progress-updates / -seconds-between-progress-updates

Output traversal statistics every time this many seconds elapse

double 10.0 [ [ -∞ ∞ ] ]

--sequence-dictionary / -sequence-dictionary

Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.

GATKPath null

--shard-size

when running in parallel this is the suggested shard size in base pairs. The actual shard-size may vary to adapt to small contigs and the requested number of threads

int 1000000 [ [ 100 ∞ ] ]

--showHidden / -showHidden

display hidden arguments

boolean false

--sites-only-vcf-output

If true, don't emit genotype fields when writing vcf file output.

boolean false

--str-table-path / -str

location of the zip that contains the sampling sites for the reference

R GATKPath null

--threads

suggested number of parallel threads to perform the estimation, the default 0 leave it up to the VM to decide. When set to more than 1, this will activate parallel in the absence of --parallel

int 0 [ [ 0 ∞ ] ]