This would introduce a new sub tool mchap call ... which takes a VCF of assembled haplotypes as input and use those haplotypes to call genotypes from the input bam files. This is necessary (though not urgent) for the tools for polyploids initiative and will avoid adding more parameters to mchap assemble as part of #104. It is also a means to record the "raw" haplotype assemblies and then recall without performing the assembly twice.
[ ] Brute-force (exact) genotype calling from known haplotypes
timothymillar
commented
3 years ago
Related to #104
This would introduce a new sub tool
mchap call ...which takes a VCF of assembled haplotypes as input and use those haplotypes to call genotypes from the input bam files. This is necessary (though not urgent) for the tools for polyploids initiative and will avoid adding more parameters tomchap assembleas part of #104. It is also a means to record the "raw" haplotype assemblies and then recall without performing the assembly twice.mchap callmchap assemble