Ignore all non-ACGT alleles from input VCF files

iqbal-lab-org / minos

Variant call adjudication

MIT License

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Ignore all non-ACGT alleles from input VCF files #117

Closed martinghunt closed 2 years ago

martinghunt commented 2 years ago

See https://github.com/iqbal-lab-org/minos/issues/116#issuecomment-1207988087

From VCF spec 4.3: "ALT field must be a symbolic allele, or a breakend replacement string, or match the regular expression ^([ACGTNacgtn]+|\*|\.)$."

We only want to consider ACGT alleles, and so discard any alleles that do not match this regex: ^[ACGTacgt]+$.

martinghunt commented 2 years ago

fixed in commit 0d3909e0935a78e4cd1476a51ffc569a82a2e238