sav export vcf / AF is updated MAF not
ilarsf opened this issue · 2 comments
Hi Jonathon,
when I export a subset with
sav export --sample-ids <SAMPLE ID> --file-format vcf <in.sav> <out.vcf>
I found that savvy updated the INFO/AF which is a great feature. However, the INFO/MAF remained unchanged.
FYI: I'm using the latest savvy version in your home directory
Cheers,
Lars
Yeah, I can add MAF to the auto-generated fields. Currently, it's only AC, AN and AF for GT data and AF for HDS.
Fixed in 5bdc408.
Note: A new option (--update-info) has been added to import and export. The default is auto, but it can also be set to always or never. Auto will update the info fields when subsetting samples, so there is no need to actually specify --update-info unless you need to force update a file with incorrect info fields.