Question on joint genotyping

[ldorozco]

I as wondering if AsmVar does "joint genotyping" of multiple samples, analogous to what GATK does for SNPs?

Does AsmVar do break-point resolution? For example, if I have a population samples with structural variants in the same region, can AsmVar use that information to try to figure out the boundaries of the structural variant?

Thank you,

Luz

[ShujiaHuang]

Hi @ldorozco , AsmVar does "joint genotyping" using Gaussian mixture model, different from the exact algorithm by GATK. AsmVar calls structural variant in break-point resolution since it calls variants from an de novo assembly. You must have the population samples assembled so as to figure out the boundaries of the structural variant.

[ldorozco]

Hi, Thank you for your reply. I have one quick follow up. Does the genotyping option for AsmVar work only for variants called by AsmVar, or can it do joint genotyping given variants in a population sample? Thank you for your time. Luz

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On Mon, Jul 24, 2017 at 2:16 AM, YellowTree ***@***.***> wrote: Hi @ldorozco <https://github.com/ldorozco> , AsmVar does "joint genotyping" using Gaussian mixture model, different from the exact algorithm by GATK. AsmVar calls structural variant in break-point resolution since it calls variants from an de novo assembly. You must have the population samples assembled so as to figure out the boundaries of the structural variant. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEEiyUp7JCb87j3pQEuaf_uXeI6r5Dsuks5sRGDVgaJpZM4Oeu3s> .