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**EXPERIMENTAL** FilterVariantTranches

Apply tranche filtering

Category Variant Evaluation and Refinement


Overview

Apply tranche filtering to VCF based on scores from the INFO field.

Inputs

  • The input variants to tranche filter.
  • snp-truth-vcf A VCF containing known common SNP sites
  • indel-truth-vcf A VCF containing known and common INDEL sites.
  • info-key The key from the INFO field of the VCF which contains the values that will be used to filter.
  • tranche List of percent sensitivities to the known sites at which we will filter. Must be between 0 and 100.

Outputs

  • A tranche filtered VCF.

Usage example

Apply tranche filters based on CNN_1D scores

 gatk FilterVariantTranches \
   -V input.vcf.gz \
   --snp-truth-vcf hapmap.vcf \
   --indel-truth-vcf mills.vcf \
   --info-key CNN_1D \
   --tranche 99.9 --tranche 99.0 --tranche 95 \
   --max-sites 8000 \
   -O filtered.vcf
 

FilterVariantTranches 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
--indel-truth-vcf
null Input file of known common INDEL sites.
--output
 -O
null Output VCF file
--snp-truth-vcf
null Input file of known common SNP sites.
--variant
 -V
null Input VCF file
Optional Tool Arguments
--arguments_file
[] read one or more arguments files and add them to the command line
--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
--info-key
CNN_1D The key must be in the INFO field of the input VCF.
--max-sites
1200 Maximum number of truth VCF sites to check.
--tranche
 -t
[99.9, 99.0, 90.0] The levels of truth sensitivity at which to slice the data. (in percents, i.e. 99.9 for 99.9 percent and 1.0 for 1 percent)
--version
false display the version number for this tool
Optional Common Arguments
--gatk-config-file
null A configuration file to use with the GATK.
--QUIET
false Whether to suppress job-summary info on System.err.
--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.


--arguments_file / NA

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

List[File]  []


--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


--indel-truth-vcf / -indel-truth-vcf

Input file of known common INDEL sites.

R String  null


--info-key / -info-key

The key must be in the INFO field of the input VCF.

String  CNN_1D


--max-sites / -max-sites

Maximum number of truth VCF sites to check.

int  1200  [ [ -∞  ∞ ] ]


--output / -O

Output VCF file

R String  null


--QUIET / NA

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

Boolean  false


--showHidden / -showHidden

display hidden arguments

boolean  false


--snp-truth-vcf / -snp-truth-vcf

Input file of known common SNP sites.

R String  null


--TMP_DIR / NA

Undocumented option

List[File]  []


--tranche / -t

The levels of truth sensitivity at which to slice the data. (in percents, i.e. 99.9 for 99.9 percent and 1.0 for 1 percent)

List[Double]  [99.9, 99.0, 90.0]


--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


--variant / -V

Input VCF file

R String  null


--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


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