Vcf files with "chr" in CHROM already

hammerlab / vcf-annotate-polyphen

A tool to annotate human VCF files with PolyPhen2 effect measures

Apache License 2.0

9 stars 6 forks source link

Vcf files with "chr" in CHROM already #4

Closed pwwang closed 4 years ago

pwwang commented 4 years ago

https://github.com/hammerlab/vcf-annotate-polyphen/blob/efcf086ec537075d4677f539af4c1c4dcdfbcdad/vap/cli.py#L52

Can we patch this to the above line

'chr{}'.format(v.CHROM.replace('chr', '')),

'chr{}'.format(v.CHROM) if not v.CHROM.startswith('chr') else v.CHROM,

to adopt vcf files with chr in CHROM already?

armish commented 4 years ago

sure @pwwang -- feel free to send a PR my way (the second solution would be much better). Sorry that I wasn't handling this case as this annotator was only tested on one type of VCF.

Having said that, this package/annotation is really old. In case you want to annotate your VCFs, I would recommend going with a more recent implementation, such as https://github.com/brentp/vcfanno

armish commented 4 years ago

closed via #5