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qa should be calculated based on BCFtools consensus sequence #13

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mcarrara-bioinfo opened this issue Apr 6, 2023 · 0 comments
Open

qa should be calculated based on BCFtools consensus sequence #13

mcarrara-bioinfo opened this issue Apr 6, 2023 · 0 comments

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@mcarrara-bioinfo
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After the update of the Vpipe consensus sequence calculation rules to BCFTools, the scripts performing QA should be updated to use the new consensus.bcftools_aligned.fasta to ensure consistency.

Mainly, the changes are related to working/gather1qa, which has hardcoded filenames and relies on additional files specific for the older consensus sequences (e.g. the files with extension .matcher)
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