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Handling coverage files derived from vcf files #12

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xiaoh11 opened this issue Jan 17, 2024 · 1 comment
Closed

Handling coverage files derived from vcf files #12

xiaoh11 opened this issue Jan 17, 2024 · 1 comment

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@xiaoh11
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xiaoh11 commented Jan 17, 2024

Desired State

Need to have scripts that handle generating and pruning coverage data from VCFs instead of depth files from mpileup.

Context

Getting VCFs from CARTaGENE WGS. Have to compute depth from the raw vcfs instead of using mpileup with crams. As a result, only the mean is calculated and the median is not available.
@xiaoh11 xiaoh11 mentioned this issue Jan 17, 2024
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@grosscol
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Closed by #13

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@grosscol @xiaoh11