Hi,
I am just trying to find why the VCF file (via Freebayes) does not include GQ?
Only the following is output:
GT:DP:AD:RO:QR:AO:QA:GL
Is there a way to process the VCF to add GQ? Or have I made an error during the initial variant calling? Is there a way to amend this please so that I can access GQ scores?
Thank you for your help
Hi @abbi
maybe try the following during FreeBayes job setup:
Choose parameter selection level > Full list of options
Algorithmic features > Set Algorithmic features
Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output > change to Yes.
Hope that helps.
Kind regards,
Igor
Thank you so much!