Ideas

[milkschen]

• chain -> paf
• paf -> chain
• chain -> vcf
• vcf -> chain
• chain -> sam
• containment
• add a segment
• filter by size
• filter by overlap

[milkschen]

filter infra is ready

[milkschen]

to_paf WIP is pushed; need to test

[nhansen]

sam->chain is easier than vcf->chain, since VCF doesn't contain the endpoints of the chain alignments, only the variants within the chains. I can give sam->chain a try, though

[milkschen]

I guess sam->chain is a less common use case? At least I haven't thought of one.

Regarding vcf->chain, I used bcftools consensus -c <out.chain> -f <fasta> -o <out.fa> <vcf> to convert a VCF to a chain. The chain file is a side product by this bcftools consensus but this is pretty useful.

[nhansen]

Interesting! I never knew bcftools consensus had that option