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GATK command for adding known vcf file for SNP's so as to filter it out

I want to add a known vcf file of snps maybe from one of the databases of snp and want to remove those snp's if they also occur in my sample. How can I do this in GATK.

Also I am interested in A-->G mutations, but on the reverse strand this would be a T-->C mutation which I would like to capture of course. How can I get to know the strand specificity.

Hope to hear soon.



Best Answer


  • SheilaSheila Broad InstituteMember, Broadie admin

    Hi Varun,

    To add a known SNPs file, you can use VariantAnnotator. To remove the sites that occur both in your VCF and the known SNPs VCF, you can use SelectVariants.

    Can you please clarify what exactly you mean by your last question? What do you mean "How can I get to know the strand specificity"?


  • gupta567varungupta567varun NYMember

    Hi Sheila,
    In the VCF file, ref and the alt base are with respect to forward strand right? So if A-->G change occurs from ref to alt on the plus strand but A-->G would be a T-->C change on the reverse but it will be written as T-->C in the vcf file. How can i extract that. Am i still not clear?



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