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convert gvcf to vcf #16

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jharri34 opened this issue Feb 23, 2017 · 3 comments
Open

convert gvcf to vcf #16

jharri34 opened this issue Feb 23, 2017 · 3 comments
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jharri34 commented Feb 23, 2017 •
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@jharri34 jharri34 added the ready label Mar 1, 2017
@smchuks smchuks self-assigned this Mar 3, 2017
@smchuks smchuks removed the ready label Mar 3, 2017
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i haven't seen any progress on this card in over a month, im taking over

@jharri34 jharri34 self-assigned this Mar 26, 2017
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smchuks commented Mar 31, 2017

Can we not go straight from bam to vcf using BAI and the GATK? Is there a need for the intermediate step of going to gcvf?

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smchuks commented Mar 31, 2017

Nevermind, I see now that gcvf is needed during the variant calling step. HaplotypeCaller is ran on each sample in gcvf mode which produces the gcvf format.

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