jvarkit

VcfGatkEval

Eval/Plot gatk INFO tags for filtering

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar vcfgatkeval  [options] Files

Usage: vcfgatkeval [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -I, --input-type
      input type. vcf: vcf file or stdin. table: stdin or one or more output 
      of *.output.table.txt
      Default: vcf
      Possible Values: [vcf, table]
    -o, --output
      filename prefix
      Default: gatk.eval
    -p, --percentile
      GATK Filters should be applied to this percentile: f < x < (1.0 -f)
      Default: 0.025
    --version
      print version and exit
    --depth, --with-depth
      include INFO/DP
      Default: false

Keywords

• vcf
• gatk

Creation Date

20230424

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfgatkeval/VcfGatkEval.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite vcfgatkeval ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Run on one vcf

$ bcftools view in.bcf | java -jar dist/jvarkit.jar  vcfgatkeval -o "out1"

list output

$ ls out1.*
out1.output.filters.txt
out1.output.R 
out1.output.table.txt

plot barplots:

R --vanilla --no-save < out1.output.R 

filters for gatk that can be used using gatk --arguments_file

cat  out1.output.filters.txt

-filter
"vc.isSNP() && FS > 21.0"
--filter-name
FS_HIGH_SNP
-filter
"vc.isSNP() && MQ < 60.0"
--filter-name
MQ_LOW_SNP
-filter
"vc.isSNP() && MQRankSum < 0.0"
--filter-name
MQRankSum_LOW_SNP
-filter
"vc.isSNP() && MQRankSum > 0.0"
--filter-name
MQRankSum_HIGH_SNP
-filter
"vc.isSNP() && QD < 1.0"
--filter-name
QD_LOW_SNP
-filter
"vc.isSNP() && ReadPosRankSum < -2.2"
--filter-name
ReadPosRankSum_LOW_SNP
-filter
"vc.isSNP() && ReadPosRankSum > 2.4"
--filter-name
ReadPosRankSum_HIGH_SNP
-filter
"vc.isSNP() && SOR > 3.5"
--filter-name
SOR_HIGH_SNP

use with gatk variantFilteration:

gatk VariantFiltration -V in.vcf.gz -R reference.fasta -O out.vcf.gz --arguments_file out1.output.filters.txt

Parallelisation

run in parallel

$ bcftools view in.bcf chr1 | java -jar dist/jvarkit.jar  vcfgatkeval -o "out1"
$ bcftools view in.bcf chr2 | java -jar dist/jvarkit.jar  vcfgatkeval -o "out2"

and then concat:

cat out1.output.table.txt out2.output.table.txt  |  java -jar dist/jvarkit.jar  vcfgatkeval --input-type table  -o "out3"

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