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 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 HaplotypeCaller --dragstr-params-path.
Additional Information
Read filters
This Read Filter is automatically applied to the data by the Engine before processing by CalibrateDragstrModel.
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 | |
| --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).
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
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.
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] []
--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 ∞ ] ]
--tmp-dir
Temp directory to use.
GATKPath null
--use-jdk-deflater / -jdk-deflater
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
--use-jdk-inflater / -jdk-inflater
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
--verbosity / -verbosity
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
- ERROR
- WARNING
- INFO
- DEBUG
LogLevel INFO
--version
display the version number for this tool
boolean false
GATK version 4.2.4.0-SNAPSHOT built at Thu, 16 Dec 2021 11:57:48 -0800.
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