The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
Strang alternating GQ=0, GQ=99 calls in g.vcf
I was looking at a g.vcf file, and I noticed that there are many alternating calls, with one having GQ of 99, and the next having a GQ of 0. Looking at the other fields, I can find no reason why the GQ of these calls should alternate like that.
For example, these two calls are adjacent, and cover only one position each. The only difference appears to be that the GQ=0 call has a slightly higher read depth
gi|194447306|ref|NC_011083.1| 25644 0 A <NON_REF> 0 0 END=25644 GT:DP:GQ:MIN_DP:PL 0:34:99:34:0,1391 gi|194447306|ref|NC_011083.1| 25645 0 G <NON_REF> 0 0 END=25645 GT:DP:GQ:MIN_DP:PL 0:35:0:35:0,0
Here, the GQ=0 call actually spans more positions, and has a higher depth then the GQ=99 call
gi|194447306|ref|NC_011083.1| 25646 0 T <NON_REF> 0 0 END=25646 GT:DP:GQ:MIN_DP:PL 0:35:99:35:0,1480 gi|194447306|ref|NC_011083.1| 25647 0 C <NON_REF> 0 0 END=25655 GT:DP:GQ:MIN_DP:PL 0:39:0:35:0,0
This pattern repeats throughout the file, can someone point me to an explanation as to why this is?