Showing tool doc from version 4.0.4.0 | The latest version is 4.1.2.0

**BETA** PostprocessGermlineCNVCalls

Postprocesses the output of GermlineCNVCaller and generates VCF files.

Category Copy Number Variant Discovery


Overview

Postprocesses the output of GermlineCNVCaller and generates VCF files.

This tool generates "intervals" and "segments" VCF files that serve complementary purposes. The intervals VCF file provides a detailed listing of the most likely copy-number call for each genomic interval included in the call-set, along with call quality, call genotype, and the phred-scaled posterior probability vector for all integer copy-number states. Given that CNV events often span several consecutive intervals, it may be desirable to coalesce contiguous intervals with the same copy-number call into a constant copy-number segments. This tool further performs segmentation and genotyping by calling a dedicated python script in `gcnvkernel`. The segmentation algorithm further provides various quality metrics for the segment.

For both VCF outputs, the CNV genotype is determined as follows: the alternative allele for a CNV call is either <DEL> or <DUP>, depending on whether the most likely copy-number call is below or above the reference copy-number for the contig. The user may specify the reference copy-number state on autosomal contigs using the argument autosomal-ref-copy-number. The list of allosomal contigs may also be specified via the argument allosomal-contig. All undeclared contigs are assumed to be autosomal. The reference copy-number on an allosomal contig is determined by the sex karyotype of the sample and is set to the pre-determined contig ploidy state fetched from the output calls of DetermineGermlineContigPloidy.

Required inputs:

  • A list of paths to GermlineCNVCaller calls shards
  • A list of paths to GermlineCNVCaller model shards
  • Path to the output calls of DetermineGermlineContigPloidy
  • Index of the sample in the call-set (which is expected to be the same across all shards)
  • Output path for writing the intervals VCF
  • Output path for writing the segments VCF

The calls or model shards can be specified in arbitrary order.

Usage example

   gatk PostprocessGermlineCNVCalls \
     --calls-shard-path path/to/shard_1-calls
     --calls-shard-path path/to/shard_2-calls
     --model-shard-path path/to/shard_1-model
     --model-shard-path path/to/shard_2-model
     --sample-index 0
     --autosomal-ref-copy-number 2
     --allosomal-contig X
     --allosomal-contig Y
     --output-genotyped-intervals sample_0_genotyped_intervals.vcf
     --output-genotyped-segments sample_0_genotyped_segments.vcf
 

PostprocessGermlineCNVCalls 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
--calls-shard-path
[] List of paths to GermlineCNVCaller call directories.
--contig-ploidy-calls
null Path to contig-ploidy calls directory (output of DetermineGermlineContigPloidy).
--model-shard-path
[] List of paths to GermlineCNVCaller model directories.
--output-genotyped-intervals
null Output intervals VCF file.
Optional Tool Arguments
--allosomal-contig
[] Contigs to treat as allosomal (i.e. choose their reference copy-number allele according to the sample karyotype).
--arguments_file
[] read one or more arguments files and add them to the command line
--autosomal-ref-copy-number
2 Reference copy-number on autosomal intervals.
--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).
--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.
--gcs-max-retries
 -gcs-retries
20 If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--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
--output-genotyped-segments
null Output segments VCF file.
--reference
 -R
null Reference sequence
--sample-index
0 Sample index in the call-set (must be contained in all shards).
--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-sequence-dictionary-validation
false If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
--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
null A configuration file to use with the GATK.
--input
 -I
[] BAM/SAM/CRAM file containing reads
--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
--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
null Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
--TMP_DIR
[] Undocumented option
--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


--allosomal-contig / NA

Contigs to treat as allosomal (i.e. choose their reference copy-number allele according to the sample karyotype).

List[String]  []


--arguments_file / NA

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

List[File]  []


--autosomal-ref-copy-number / NA

Reference copy-number on autosomal intervals.

int  2  [ [ 0  ∞ ] ]


--calls-shard-path / NA

List of paths to GermlineCNVCaller call directories.

R 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  [ [ -∞  ∞ ] ]


--contig-ploidy-calls / NA

Path to contig-ploidy calls directory (output of DetermineGermlineContigPloidy).

R File  null


--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


--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


--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]  []


--gatk-config-file / NA

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  [ [ -∞  ∞ ] ]


--help / -h

display the help message

boolean  false


--input / -I

BAM/SAM/CRAM file containing reads

List[String]  []


--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


--model-shard-path / NA

List of paths to GermlineCNVCaller model directories.

R List[File]  []


--output-genotyped-intervals / NA

Output intervals VCF file.

R File  null


--output-genotyped-segments / NA

Output segments VCF file.

File  null


--QUIET / NA

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[String]  []


--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

String  null


--sample-index / NA

Sample index in the call-set (must be contained in all shards).

int  0  [ [ 0  ∞ ] ]


--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.

String  null


--showHidden / -showHidden

display hidden arguments

boolean  false


--TMP_DIR / NA

Undocumented option

List[File]  []


--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 / NA

display the version number for this tool

boolean  false


Return to top


See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum

GATK version 4.0.4.0 built at 23-40-2018 11:40:56.