Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios

Category Copy Number Variant Discovery

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Overview

Postprocesses the output of GermlineCNVCaller and generates VCF files as well as a concatenated denoised copy ratio file.

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.

Finally, the tool concatenates posterior means for denoised copy ratios from all the call shards produced by the GermlineCNVCaller into a single file.

Python environment setup

The computation done by this tool, aside from input data parsing and validation, is performed outside of the Java Virtual Machine and using the gCNV computational python module, namely gcnvkernel. It is crucial that the user has properly set up a python conda environment with gcnvkernel and its dependencies installed. If the user intends to run PostprocessGermlineCNVCalls using one of the official GATK Docker images, the python environment is already set up. Otherwise, the environment must be created and activated as described in the main GATK README.md file.

Advanced users may wish to set the THEANO_FLAGS environment variable to override the GATK theano configuration. For example, by running THEANO_FLAGS="base_compiledir=PATH/TO/BASE_COMPILEDIR" gatk PostprocessGermlineCNVCalls ..., users can specify the theano compilation directory (which is set to $HOME/.theano by default). See theano documentation at http://deeplearning.net/software/theano/library/config.html.

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
• Output path for writing the concatenated denoised copy ratios

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
     --output-denoised-copy-ratios sample_0_denoised_copy_ratios.tsv
 

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Additional Information

Read filters

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

• WellformedReadFilter

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-denoised-copy-ratios	null	Output denoised copy ratio file.
--output-genotyped-intervals	null	Output intervals VCF file.
--output-genotyped-segments	null	Output segments 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.
--disable-sequence-dictionary-validation	false	If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
--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.
--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
--reference  -R	null	Reference sequence
--sample-index	0	Sample index in the call-set (must be contained in all shards).
--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	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	null	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.

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

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

boolean  true

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--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

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

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

boolean  true

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--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

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--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

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--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

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--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]  []

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--gatk-config-file / NA

A configuration file to use with the GATK.

String  null

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--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 / NA

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.

String  ""

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--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

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--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-denoised-copy-ratios / NA

Output denoised copy ratio file.

R File  null

---

--output-genotyped-intervals / NA

Output intervals VCF file.

R File  null

---

--output-genotyped-segments / NA

Output segments VCF file.

R 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

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--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

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--sites-only-vcf-output / NA

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

boolean  false

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--tmp-dir / NA

Temp directory to use.

GATKPathSpecifier  null

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--use-jdk-deflater / -jdk-deflater

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false

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--use-jdk-inflater / -jdk-inflater

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false

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--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

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--version / NA

display the version number for this tool

boolean  false

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GATK version 4.1.4.1 built at Thu, 5 Dec 2019 09:51:56 -0500.