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align2alleles.py will skip fixed variants when --min-allele-count is greater than 1 #52

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jts opened this issue Nov 10, 2020 · 0 comments

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jts commented Nov 10, 2020

When align2alleles.py is called with --min-allele-count > 1 and a SNP is present in all samples, the reference allele will not be included here:

https://github.com/jts/ncov-tools/blob/master/workflow/scripts/align2alleles.py#L82

This is not unintuitive so should be changed so the reference allele is always included

jts self-assigned this

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