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extract heterozygotes from the vcf before converting to h5 files #63

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aryarm opened this issue Jan 8, 2021 · 1 comment
Open

extract heterozygotes from the vcf before converting to h5 files #63

aryarm opened this issue Jan 8, 2021 · 1 comment
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enhancement New feature or request

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@aryarm
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aryarm commented Jan 8, 2021

instead of downstream in the counts subworkflow

Homozygotes aren't useful in allele-specific analyses, so we discard them in the counts subworkflow. But discarding them upstream, even before running WASP, might significantly speed up execution of the pipeline. So are there any downsides to this?

@aryarm aryarm added the enhancement New feature or request label Jan 8, 2021
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aryarm commented Jan 12, 2021

actually, it turns out that extracting heterozygotes from the vcf is the last step in the variant calling pipeline

so we should

  • add a comment to the wasp and counts configs (and their documentation) that encourages users to extract heterozygotes from their VCFs before passing the variants into our pipeline

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