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Rare variants from annotated vcf file

rohan1925rohan1925 New YorkMember
edited February 2014 in Ask the GATK team


I have annotated my vcf file of 20 samples from Unified genotyper using the following steps.

Unified genotyper->Variantrecalibration->Applyrecalibration->VariantAnnotator

My question is how should I proceed if I have to select rare variants (MAF<1%) for the candidate genes that I have,for each of these 20 samples?

Post edited by rohan1925 on


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    edited February 2014

    Hi there,

    If you're asking how you should design your analysis, I'm afraid this question is beyond our current scope of support. I can only point you to the variant manipulation tools (e.g. SelectVariants) and answer specific questions about how to use them.

  • rohan1925rohan1925 New YorkMember
    edited February 2014

    I want to use SelectVariants only since I have used all the tools from GATK until Variant Annotator for variants.So in this how should I get MAF (minor allele frequency) to be less than 1%,using -AF parameter?

    Also,I need to select variants only for candidate genes that I have.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Ah, sorry to get back to you so late. I believe you should be able to do that simply using -select "AF < 0.01". Let me know if that doesn't work for you.

  • rohan1925rohan1925 New YorkMember


    Thanks for your response! I am using this command,and getting some error.

    java -Xmx2g -jar /GenomeAnalysisTK-2.7-4-g6f46d11/GenomeAnalysisTK.jar -T SelectVariants -R human_g1k_v37.fasta --variant annotated.vcf -o -select "AF<0.01"

    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace

    java.lang.IllegalArgumentException: Invalid JEXL expression detected for select-0 with message ![0,9]: 'AF < 0.01;' < error

    In my VariantRecalibration,I had asked for following parameters to be included:
    -an DP -an QD -an FS -an MQRankSum -an ReadPosRankSum

    Do I have to include -an AF as well?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    No, if it was a problem of missing annotations the error would be different. Is there any chance some of your variants are multi-allelic? The problem is that for multi-allelic variants, AF is a list of numbers instead of a single number, so the JEXL expression I gave you won't work. Unfortunately there is currently no way to test AF for multi-allelic variants, so you need to skip them in order for this to work.

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