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Variant Filter

nansnans Member
edited March 2017 in Ask the GATK team

I have generated a multi sample vcf file with haplotype caller followed by CombineGVFs -> VariantReCalibrator -> Apply Recalibration.

Now I would like to filter my variants (only SNPs) based on GQ, DP and allele depth ->
AD for homozygous alt calls,
for homozygous ref calls and
for heterozygous calls.

I know how to filter based on GQ/DP but for allele depth, is there a way of doing this? I'm not able to find a filter expression on allele depth, obviously, I am missing on something!

Thank you

Post edited by nans on

Best Answer


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    I think you will find this article helpful (particularly under Using JEXL to evaluate arrays).


  • nansnans Member
    edited March 2017

    Hi @Sheila,

    Thank you. But as far as I understand the article you shared, it is for one sample at a time. Can this handle 1500 samples together ?

    Thank you.

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