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harrispopgen / mutyper

Ancestral k-mer mutation types for SNP data
https://harrispopgen.github.io/mutyper/
MIT License
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Changed the 'number' type of 'mutation type' to A in the VCF header #35

Closed Lukez-pi closed 2 years ago

Lukez-pi commented 2 years ago

Changed the 'Number' type of 'mutation type' from '1' to 'A' in the VCF header. This is useful because in the case of merging bi-allelic variants into a single multi-allelic variant in a VCF file, 'Number' type of 1 will overwrite the previous 3mer mutation type, whereas type 'A' will append.

wsdewitt commented 2 years ago

Thanks @Lukez-pi. I can see this small change (one character!) will allow you to merge mutyper-annotated biallelic calls from the same site into a mutliallelic variant with mutation type info for each alt allele (using bcftools norm). If you are interested in enabling mutyper to run directly on multiallelic snps, I think those modifications would be straightforward (although more than one character). Do you want that, or do you want to leave it at this?

Lukez-pi commented 2 years ago

I am content with leaving it as a single change for now. Would it be appropriate to open "enable direct processing of multi-allelic SNPs" as an issue, so that I can take a crack at it later?

wsdewitt commented 2 years ago

Yes, please do open an issue for that.