Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

can VariantsToTable output the raw genotype call (i.e., 0/1) rather than the actual basecall (A/T)?

mmats010mmats010 Riverside CAMember

I'm interested in getting simple "heterozygous" or "homozygous" designations for all of the samples/SNPs in my multisample VCF file. In the past, I have been using the -GF GT option in VariantsToTable, and then annotating my basecalls in Excel as either heterozygous or homozygous. This takes forever since Excel isn't really built for big data like this. Is there a simple way to output all of the SNPs as 0/1, 0/0, 0/1, or 1/1 instead of C/A, A/A, G/T, C/C?

Best Answer

Answers

  • mmats010mmats010 Riverside CAMember

    Thanks, Not sure why I missed that thread. I also found a workaround.

    By running

    grep -v ^## input.vcf | cut -f1,2,10- | sed 's/:\S*//g' > output.txt

    It reported exactly what I needed. However, I'm not sure how much of a grain of salt I should take this result with given the Broad's insistence on using a dedicated tool to parse a VCF file as opposed to doing it manually. It seems to have worked as expected for the time being.

    -Mike

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @mmats010 The main reason why we push VariantsToTable as opposed to manual parsing is that we've seen so many people lose time and effort due to unexpected/silent failures using manual parsing solutions - particularly when they're trying to do something a little complicated that is vulnerable to weird VCF idiosyncrasies. In your case you're doing something that's simple enough that I wouldn't worry about it.

  • Is there still no tool/method to address this question? My genotype fields are very complex so manual parsing with sed is not a safe thing to do.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @Erythroxylum
    Hi,

    No, the behavior has not changed in GATK4. I don't think there are any plans to change it any time in the near future.

    -Sheila

Sign In or Register to comment.