Ideas - Githubissues

milkschen / chaintools

Utilities for the genomic chain format

MIT License

6 stars 2 forks source link

Ideas #1

Open milkschen opened 2 years ago

milkschen commented 2 years ago

[x] chain -> paf
[ ] paf -> chain
[x] chain -> vcf
[ ] vcf -> chain
[x] chain -> sam
[ ] containment
[ ] add a segment
[x] filter by size
[x] filter by overlap

milkschen commented 2 years ago

filter infra is ready

milkschen commented 2 years ago

to_paf WIP is pushed; need to test

nhansen commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

Interesting! I never knew bcftools consensus had that option