Question

How to get GQ after running BCFTools?

2

Entering edit mode

9.3 years ago

Tails ▴ 80

New version of BCFTools (using call instead of view) doesn't produce VCF files with GQs in the FORMAT field.

Does anyone know how to get it in the new version (1.1)?

sequencing SNP • 3.5k views

ADD COMMENT • link updated 9.1 years ago by timothee.cezard ▴ 50 • written 9.3 years ago by Tails ▴ 80

score 5 · Accepted Answer · 2015-03-06

5

Entering edit mode

9.1 years ago

timothee.cezard ▴ 50

When you run bcftools call specify -f GQ to have it added to the output

 bcftools call -vmO z -f GQ

ADD COMMENT • link 9.1 years ago by timothee.cezard ▴ 50