Which GATK tool should I use? - VariantFiltration exomeseq

Question

[wiki97]

GATK VariantFiltration

Hi, I would like to filter variants for quality check, variants were called with MuTect2.

I want to apply the following parameters:

Quality Depth (QD) >2 
Mapping Quality (MQ) > 40
Fisher test of strand bias (FS) < 60 
MQRankSum > -12.5 
ReadPosRankSum > -8

My question is - which GATK tool should I use?

I thought that VariantFiltration should be used here, however if I understood well the GATK overview - VariantFiltration only filters variants basing on those criteria but it doesn't calculate the QD, MQ, FS etc. criteria itself, am I right?

I am new to exome-seq and will be grateful for any help :)

Answer 1

[Pierre Lindenbaum]

all those INFO can be added witn GATK VariantAnnotator and the option -A

One or more specific annotations to add to variant calls

e.g: https://gatk.broadinstitute.org/hc/en-us/articles/360036349292-MappingQuality

https://gatk.broadinstitute.org/hc/en-us/articles/360036728131-DepthPerSampleHC

etc...

[wiki97]

Dear Pierre Lindenbaum, thank you very much for your answer it worked perfectly!