Apply tranche filtering

Category Variant Filtering

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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.

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--arguments_file / NA

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

List[File]  []

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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  [ [ -∞  ∞ ] ]

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--help / -h

display the help message

boolean  false

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

Input file of known common INDEL sites.

R String  null

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--info-key / -info-key

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

String  CNN_1D

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--max-sites / -max-sites

Maximum number of truth VCF sites to check.

int  1200  [ [ -∞  ∞ ] ]

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--output / -O

Output VCF file

R String  null

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--QUIET / NA

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

Boolean  false

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--showHidden / -showHidden

display hidden arguments

boolean  false

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

Input file of known common SNP sites.

R String  null

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--TMP_DIR / NA

Undocumented option

List[File]  []

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--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]

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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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--variant / -V

Input VCF file

R String  null

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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 4.0.5.1 built at 25-59-2019 01:59:53.