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Input VCF files need to be in a certain format? #6

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Kelzor opened this issue Sep 7, 2020 · 1 comment
Open

Input VCF files need to be in a certain format? #6

Kelzor opened this issue Sep 7, 2020 · 1 comment

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@Kelzor
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Kelzor commented Sep 7, 2020

Hello!

Do the VCF files need to have been generated by UnifiedGenotyper/EAGER, or can MUSIAL interpret VCFs from freebayes or HaplotypeCaller?

Thanks,
Kelly
@alex-seitz
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Hi Kelly,
MUSIAL uses the htsjdk-library to parse the vcf-Files.
If I remember correctly, it has problems with freebayes for some reason. Everything generated with GATK should be fine tough.

Best,
Alex

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@alex-seitz @Kelzor