Open janaobsteter opened 10 months ago
We discussed in one of the meetings how we could convert multi-allelic sites to multiple bi-allelic sites. My understanding was that bcftools enables this conversion. Would that help?
For now, let's filter the VCF to only keep biallelic SNPs to see how it behaves and then we can progress with adding other types of variants in the future.
In the ancestral allele inference, we filter the variants for SNPs, but we do allow multi-allelic SNPs since that is not a problem for the ancestral inference (it's just an allele count). However, some rule might fall if there are multiallelic variants in the VCF and the INFO file (for example, the
get_major
rule inprepare_files_for_tsinfer.smk.