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Genotypes and VariantsToTable walker

sanderpajusalusanderpajusalu Tartu, EstoniaMember


I just started using VariantsToTable tool, which works great. I am still facing a problem with genotype fields extracted from vcf as the numbered genotypes (0/1) are changed to nucleotides (T/C). That is something that I do not want. Therefore, I would like to ask, if there is a way to stop this happening, so that the walker leaves genotypes to number format as they are in vcf file?

Thank you!


Best Answer


  • sanderpajusalusanderpajusalu Tartu, EstoniaMember


    Thank you for your answer! However, maybe you would consider making an extra command argument in future GATK releases that allows to choose whether you want genotypes as numbers or nucleotides...


  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭


    Hi Sander,

    Unfortunately, our developers are too busy with higher priority items to implement this right now. However, if you or someone else makes a patch to add that capability, we are definitely willing to look at it.


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