SVtyper for SNVs/indels

hall-lab / svtyper

Bayesian genotyper for structural variants

MIT License

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SVtyper for SNVs/indels #94

Closed fpbarthel closed 6 years ago

fpbarthel commented 6 years ago

Hi,

I'm a big fan of svtyper for SV workflows and wondering if there is a tool that does the same for SNVs/small indels. Eg. given a set of variants defined according to the first eight columns (CHROM to INFO) of a VCF file, output the FORMAT field for any number (n) of given BAM files.

Floris

ernfrid commented 6 years ago

SNV/Indel calling isn't a field that I keep on top of anymore, but I do believe that freebayes has similar functionality. See https://github.com/ekg/freebayes#examples

fpbarthel commented 6 years ago

Thanks!