Hello,

I obtained a vcf file as an output of the populations module of Stacks v2.4.1 (Catchen, 2013). In the INFO section, I only have the flags NS (i.e number of sample with data) and AF (i.e allele freq).

My question is simple: How can I compute or somehow add other INFO flags to this vcf, like : AB, the allele balance DP, the site depth MQM and MQMR, for mapping qualities SAF, the strand balance PAIRED, for the properly paired status

These flags would help me to filter the vcf later on.

Thanks!

Noé