Haplotype caller, multisample calling on set of 9 solid and 1 ilumina sample

WimSWimS Posts: 25Member

How does the haplotype caller handle multiple samples? Does it do a local denovo assembly for every sample and then compare those or does it do 1 local denovo assembly using the reads of all the samples?

Can I run the haplotype caller on a set of 9 solid (50bp fragment and 50 x 35 PE) together with 1 ilumina sample (100 x 100 PE) ?

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  • bmoneybmoney Posts: 2Member

    Hello Geraldine,

    Is there any particular reason you can think of as to why we should not use HaplotypeCaller on SOLiD data?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,019Administrator, GATK Dev admin

    No, it should be fine. It's just that we don't work with solid data, so we can't guarantee it works.

    Geraldine Van der Auwera, PhD

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