Keeping indels, projecting reference coordinates?

sanger-pathogens / snp-sites

Finds SNP sites from a multi-FASTA alignment file

http://sanger-pathogens.github.io/snp-sites/

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Keeping indels, projecting reference coordinates? #66

Open LovellHAGSC opened 6 years ago

LovellHAGSC commented 6 years ago

Hi there, Is there any planned (or implemented) was to analyze indels via snp-sites? Basically, I want to annotate all variants (not just snps) in my multiple-sequence alignment and project those variants against the original reference (which also has indels) coordinate system.

Thanks, John

OwenDonohoe commented 2 years ago

a response here would be appreciated