Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios
Category Copy Number Variant Discovery
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.
This tool can also take a VCF specifying breakpoints to be used instead of HMM-derived segmentation using posterior
probabilities from the intervals. This functionality enables the calculation of new quality scores using breakpoints
derived from another source, as with JointGermlineCNVSegmentation applied to multiple samples. When using this functionality,
an input-intervals-vcf
from the original PostprocessGermlineCNVCalls call without multi-sample
breakpoints should also be provided.
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
https://theano-pymc.readthedocs.io/en/latest/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 examples
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
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 --input-intervals-vcf sample_0_genotyped_intervals.vcf --clustered-breakpoints cohort_breakpoints.vcf --output-genotyped-intervals sample_0_genotyped_intervals.clustered.vcf --output-genotyped-segments sample_0_genotyped_segments.clustered.vcf --output-denoised-copy-ratios sample_0_denoised_copy_ratios.clustered.tsv -R reference.fasta
Additional Information
Read filters
This Read Filter is automatically applied to the data by the Engine before processing by PostprocessGermlineCNVCalls.
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 |
Path to contig-ploidy calls directory (output of DetermineGermlineContigPloidy). | ||
--model-shard-path |
List of paths to GermlineCNVCaller model directories. | ||
--output-denoised-copy-ratios |
Output denoised copy ratio file. | ||
--output-genotyped-intervals |
Output intervals VCF file. | ||
--output-genotyped-segments |
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). | |
--clustered-breakpoints |
VCF with clustered breakpoints and copy number calls for all samples, can be generated with GATK JointGermlineCNVSegmentation tool | ||
--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! | |
--duplication-qs-threshold |
50 | Filter out duplications with quality lower than this. | |
--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 | |
--het-deletion-qs-threshold |
100 | Filter out heterozygous deletions with quality lower than this. | |
--hom-deletion-qs-threshold |
400 | Filter out homozygous deletions with quality lower than this. | |
--input-intervals-vcf |
Input VCF with combined intervals for all samples | ||
--interval-merging-rule -imr |
ALL | Interval merging rule for abutting intervals | |
--intervals -L |
One or more genomic intervals over which to operate | ||
--reference -R |
Reference sequence | ||
--sample-index |
0 | Sample index in the call-set (must be contained in all shards). | |
--site-frequency-threshold |
0.01 | Filter out variants with site frequency higher than this. | |
--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. | ||
--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 | |
--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
--allosomal-contig
Contigs to treat as allosomal (i.e. choose their reference copy-number allele according to the sample karyotype).
List[String] []
--arguments_file
read one or more arguments files and add them to the command line
List[File] []
--autosomal-ref-copy-number
Reference copy-number on autosomal intervals.
int 2 [ [ 0 ∞ ] ]
--calls-shard-path
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 [ [ -∞ ∞ ] ]
--clustered-breakpoints
VCF with clustered breakpoints and copy number calls for all samples, can be generated with GATK JointGermlineCNVSegmentation tool
File null
--contig-ploidy-calls
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
--duplication-qs-threshold
Filter out duplications with quality lower than this.
int 50 [ [ 0 ∞ ] ]
--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
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 ""
--help / -h
display the help message
boolean false
--het-deletion-qs-threshold
Filter out heterozygous deletions with quality lower than this.
int 100 [ [ 0 ∞ ] ]
--hom-deletion-qs-threshold
Filter out homozygous deletions with quality lower than this.
int 400 [ [ 0 ∞ ] ]
--input / -I
BAM/SAM/CRAM file containing reads
List[GATKPath] []
--input-intervals-vcf
Input VCF with combined intervals for all samples
File null
--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-variants-per-shard
If non-zero, partitions VCF output into shards, each containing up to the given number of records.
int 0 [ [ 0 ∞ ] ]
--model-shard-path
List of paths to GermlineCNVCaller model directories.
R List[File] []
--output-denoised-copy-ratios
Output denoised copy ratio file.
R File null
--output-genotyped-intervals
Output intervals VCF file.
R File null
--output-genotyped-segments
Output segments VCF file.
R File null
--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
GATKPath null
--sample-index
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.
GATKPath null
--showHidden / -showHidden
display hidden arguments
boolean false
--site-frequency-threshold
Filter out variants with site frequency higher than this.
double 0.01 [ [ 0 ∞ ] ]
--sites-only-vcf-output
If true, don't emit genotype fields when writing vcf file output.
boolean false
--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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