Question

Gatk: How To Filter Variant Based On Genotype Quality (Gq)

1

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12.4 years ago

Frédéric Bigey ▴ 310

Hi, I would like to extract variants for on sample only if its genotype quality (GQ) is above cutoff.

I have tried this:

$pathToGATK \ 
  -T SelectVariants \ 
  -R ref \ 
  --variant inVCF \ 
  -sn mylib \ 
  -select "vc.getGenotype('mylib').GQ > 10.0" \ 
  --selectTypeToInclude SNP \ 
  --out outVCF

Unfortunately, this command outputs absolutely no variant (the VCF header is ok). No error message occured. Is some one could help me?

Fred

gatk • 7.7k views

ADD COMMENT • link updated 12.4 years ago by Pierre Lindenbaum 164k • written 12.4 years ago by Frédéric Bigey ▴ 310

score 4 · Answer 1 · 2012-07-11

4

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12.4 years ago

Pierre Lindenbaum 164k

As far as I understand, the GATK function getGenotype returns a java object 'Genotype':

https://github.com/broadgsa/gatk/blob/139c6b84a15d4318fd59f4c4c7922c628e4cc336/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java

The class contains a function: getPhredScaledQual()

can you try

-select "vc.getGenotype('mylib').getPhredScaledQual() > 10.0" \

ADD COMMENT • link 12.4 years ago by Pierre Lindenbaum 164k

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Thanks a lot Pierre,

It works fine now !

Reading the source code can help obvously...

FB

ADD REPLY • link 12.4 years ago by Frédéric Bigey ▴ 310

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please , flag my answer as "answered".

ADD REPLY • link 12.4 years ago by Pierre Lindenbaum 164k

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Pierre, I don't find the way to flag your answer.

ADD REPLY • link 12.4 years ago by Frédéric Bigey ▴ 310

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on the left side of my answer, under the number of votes. You must be logged. :-)