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Add possibility to run HaplotypeCaller without dbsnp #182

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merged 1 commit into from
Apr 15, 2020

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nf-core/sarek pull request

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@maxulysse maxulysse requested a review from a team April 15, 2020 15:33
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With @mahesh-panchal we're helping out a user with 96 samples of a species with only a ref genome to start with.
So the idea is actually to use Sarek to build a set of known sites.
I think that Strelka and HaplotypeCaller would be enough to generate a set of VCFs that can be filtered/merged and then used until convergence.

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@ggabernet ggabernet left a comment

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Looks good :)

@maxulysse maxulysse merged commit 411c2d5 into nf-core:dev Apr 15, 2020
@maxulysse maxulysse deleted the Bee branch April 15, 2020 15:44
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2 participants