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Referce SNPs in the same vcf file than the alternative alleles

shinkenshinken IrapuatoMember

Hi all,

I have a simple question, I have several individuals sequenced with GBS and I want to call SNPs from all of them. Using the best practice approach, that includes to run the HC in GVCF mode and then make the joint calling on multiple GVCFs I am going to end with a multisample VCF file.

What I want to know is if in the multi sample VCF file are going to be included the reference SNPs (those ones in the reference genome) and the alternative alleles. Because the nature of my individuals I expect per site the 25% with my individuals with the alternative allele and 75% with the reference allele and for me is important to call both. With these best practice process, of course If I have enough data in the site and playing with the filtering process after. I am going to be able to obtain both alleles per site? .

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Answers

  • shinkenshinken IrapuatoMember

    Thank you very much was very helpful.

    Now I have other two questions, it is supposed that there is a traditional Joint calling but I can not found any documentation or tutorials about it. Do you know if there is something to read about it and how to run it? I am also reading about the joint Genotype from the best practices here:

    https://software.broadinstitute.org/gatk/best-practices/bp_3step.php?case=GermShortWGS

    But in my case in the step by step tutorial there is this legend:

          None found. Request documentation or report a problem in the forum.
    

    Do you know where I can found the tutorial?

    Thank you

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