chrX sites count
AinaMontalban opened this issue · comments
Hello,
I am using somalier to perform sex QC on WES samples, and I have a question regarding the number of sites on chrX.
I created a VCF file containing 203 sites from chrX using our target bed file and the somalier find-sites command. Then, when I ran the command somalier extract and relate on a sample, I noticed that Somalier reports X_n as 199, even though there should be 203 sites on chrX:
| X_depth_mean | X_n | X_hom_ref | X_het | X_hom_alt |
|---|---|---|---|---|
| 81.56 | 199 | 103 | 0 | 96 |
Why are we missing 4 sites?
Initially, I thought that the -d (MIN_DEPTH) parameter might be the reason. So, I ran the HaplotypeCaller with a base-pair resolution to check the allele depth of these sites. But none of the sites had a depth of less than 7. However, 4 sites had a GQ<30:
chrX 69670203 . C <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:60,19:79:**0**:0,0,1333
chrX 119934456 . G <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:19,2:21:**1**:0,1,642
chrX 136491943 . A <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:36,10:46:**0**:0,0,923
chrX 151397088 . G <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:10,0:10:**24**:0,24,360
Does somalier exclude genotypes with low quality? Or is it something else?