Get a summary of SNV calls from MuTect2

alaabadrealaabadre FranceMember
edited March 2018 in Ask the GATK team

Hello,

Following the best practice of calling variants using MuTect2 with GATK3, I have stumbled upon the step 5 where we can filter our file for INDELs or SNPs. But I had issues with the contigs not being of the same length, so I switched to version 4 of GATK to get past the issue and successfully generated a VCF file only made of INDELs.

My question now is that how can we summarize the different results as shown in the step 5 ?

like the following :

Thanks a lot for your help.

Best regards,
Alaa

Best Answer

Answers

  • alaabadrealaabadre FranceMember

    Thank you Sheila for your answer. I think this is good enough to summarize the output.

    Best regards,
    Alaa

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