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browning-lab / hap-ibd

The hap-ibd program detects identity-by-descent segments in phased genotype data.
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feature: Read genetic distance data from the VCF directly. No map file necessary. #9

Open pettyalex opened 1 year ago

pettyalex commented 1 year ago

shapeit4 output includes cM for each marker in the INFO column, like so:

##INFO=<ID=CM,Number=A,Type=Float,Description="Interpolated cM position">

This PR adds a new flag: vcf-has-cm, which will use the genetic position reported from the VCF file, rather that needing a genetic map and interpolating. This allows directly using the reported genetic position for each marker.

I know that you prefer email, so I'm sending one with more context.