how to filter a gvcf
Hi GATK team,
I generated a gvcf file to get sequencing information for both variant and non-variant positions. I have couple of questions about how to filter out the unreliable callings.
1, in a gvcf file, I found records with all values of DP, GQ, MIN_DP and PL are 0 (see below), is it mean that this region is missing from the data (no reads were mapped to this region of reference genome)?
Scaffold10021 1 . A . . END=2870 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0
2, for case, with high depth but GQ=0. Can I trust the calling, or should set it to missing.
Scaffold10012 1189 . C . . END=1198 GT:DP:GQ:MIN_DP:PL 0/0:401:0:370:0,0,0
Scaffold10012 904 . A . . END=905 GT:DP:GQ:MIN_DP:PL 0/0:415:0:415:0,0,0
3,Which parameters were usually used to filter a gvcf file?
4, To accept a calling, what is minimum values for GQ and PL?
Thanks very much!