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Unified genotyper with multi sample : SNPs alleles for each sample

Hi, using unified genotyper with multiple samples (different lines of Medicago truncatula showing polymorphism), I would like to get a file giving me, for each sample, the alleles at each SNP position (SNP positions identified for all samples). Is it possible? I didn't find any option for this, and it would be dificult to make SNP calling for each sample and then create a new file with all of them, because SNPs positions and number are different according to the samples.
Thanks in advance,



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    I'm not sure I understand your question, but it sounds like you what you want is a multisample VCF file, which is the normal output of UnifiedGenotyper when you input multiple samples. Have you tried doing that, and if so, is the output not satisfactory?

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