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Combine SNPs and INDELs when using Haplotype Caller

Just wondering what is the best way to combine SNPs and INDELs after using Haplotype caller to get a single VCF. It seems straight forward with UnifiedGenotyper, since there is eparate VCF for each, and they are recalibrated separately. But the Haplotype caller, they are relibrated indivisually in the already combined file.
I have recalibrated SNPs and INDELs separately, but not sure how to combine them. since both recalibrated VCFs contain allvariants, not sure combineVariants can handle it.


Best Answer


  • SheilaSheila Broad InstituteMember, Broadie, Moderator


    There should be no need to make two separate VCFs in the VQSR step. Have a look at this document for more information.


  • analyst123analyst123 Boston, MAMember

    Hi, thanks for the response. I do understand that snp and indel VQSR need to be done in succession, but I have still questions on the procedure to do so.
    Once separate snp and Indel recal files have been generated, should I apply re calibration using mode snp first, then in the resulting VCF apply mode indel.

  • Michael_WeinsteinMichael_Weinstein Los AngelesMember

    I'm actually working on modifying a pipeline right now for variant calling. Here is my (slightly censored) command line for this:
    java -Xmx4g -jar GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T BaseRecalibrator -R Ref/human_g1k_v37.fasta -I indelRealigned.input.bam -knownSites Ref/dbsnp_138.b37.vcf -knownSites Ref/Mills_and_1000G_gold_standard.indels.b37.vcf -o output.recal.table

    Are you running IndelRealigner right before this, which does take only known indels and outputs a new BAM file?

  • Michael_WeinsteinMichael_Weinstein Los AngelesMember

    Ah, that's what I get for starting at BQSR all day. I'm starting to see it everywhere!

    Hi Sheila!

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