Adding priors to UnifiedGenotyper.

I don't know if this question has been asked, if so sorry.

When using UnifiedGenotyper, I was wondering if it was possible (via hidden command option, etc) to use a VCF file as a prior. Currently I have just been adding additional bam files, but it would be nice (and quicker) if I could use a Indexed file.

Thanks for your time.

Shawn.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,051Administrator, GATK Dev admin

    Hi Shawn,

    What exactly do you mean by "prior"? Do you mean you have known sites, or genotypes, that you would like the UG to use in the discovery process?

    Geraldine Van der Auwera, PhD

  • srynearsonsrynearson Posts: 2Member

    Sorry about being unclear. By prior I mean known sites, i.e. 1000G.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,051Administrator, GATK Dev admin

    You can provide known sites using the `--dbsnp' argument, but be aware that they won't be used in any calculations; they'll just be used to populate the rsID field (if your knowns have IDs annotated).

    Did you have any specific purpose in mind for using known sites, e.g. only call variants at those sites, or genotyping given alleles? There are various options to do these things, but right now I'm still not sure what you're trying to achieve so I don't know which to point you towards.

    Geraldine Van der Auwera, PhD

  • YingyaYingya Posts: 1Member

    Hi Geraldine,

    I would like the UG to use the posterior probability of a known site called from a sample as prior probability for calling variant of the corresponding site from another sample. Is the UG could do that?

    Fuqiang

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,051Administrator, GATK Dev admin

    Hi Fuqiang,

    No, that's not possible. You cannot influence the UG's calculation in this way.

    Geraldine Van der Auwera, PhD

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