Closed marchoeppner closed 3 years ago
It looks to me like the CT>C deletion did not pass the default allele quality filter applied in the DeepVariantWES
configuration. You can try running with the DeepVariant_unfiltered
configuration to confirm if that's true. In a larger cohort, another sample might exhibit the allele more confidently and thereby "rescue" its report (for all samples) in the joint VCF.
If the deletion doesn't show up in the unfiltered mode, there are a couple other things we might look into, such as do we happen to be at the edge of one of the BED target regions, or that the haplotype in question (15174241 TGG>CG) can be written in a few different ways synonymously.
Thanks for the pointer.
This is what happens with the suggested "unfiltered" config:
chr19 15174240 chr19_15174241_T_C;chr19_15174240_CT_C CT CC,C 66 . AF=0.8125,0.0625;AQ=66,20 GT:DP:AD:GQ:PL:RNC 1/1:112:0,112,0:61:65,63,0,990,990,990:.. 1/1:169:0,169,0:58:61,60,0,990,990,990:.. 1/2:78:.,78,99:8:0,0,0,0,0,0:.. 1/1:208:0,208,0:61:66,63,0,990,990,990:.. 1/1:94:0,94,0:56:58,60,0,990,990,990:.. 0/1:196:96,99,0:53:52,0,68,990,990,990:.. 1/1:156:0,156,0:57:59,60,0,990,990,990:.. 0/1:202:105,97,0:53:53,0,63,990,990,990:..
chr19 15174242 chr19_15174242_G_C G C 58 . AF=0.0625;AQ=58 GT:DP:AD:GQ:PL:RNC 0/0:112:112,0:50:0,300,2999:.. 0/0:170:170,0:50:0,300,2999:.. 0/1:177:77,100:56:58,0,60:.. 0/0:207:207,0:50:0,300,2999:.. 0/0:93:93,0:50:0,282,2819:.. 0/0:198:198,0:50:0,300,2999:.. 0/0:155:155,0:50:0,300,2999:.. 0/0:204:204,0:50:0,300,2999:..
So the variant re-appears...which is good. It just seems odd that it would be filtered, since the signal is very clear :(
GLnexus' filtering is based on DeepVariant's GQ and PL scores shown in your gVCF excerpt, which in this case are not great, not terrible (phred score ~20). The DeepVariant_unfiltered
mode may be more suitable for running with only a handful of samples as you illustrate, where the joint VCF file size and false positive rate aren't such pressing concerns. In a larger cohort, the cumulative evidence from seeing the allele in more samples would probably overcome the DeepVariantWES
reporting threshold (even if each individual observation is marginal for whatever reason).
We can separately ask why DeepVariant assigned marginal quality scores when the IGV looks pretty good. That's usually difficult to answer in view of its complex model, but I do wonder if it has something to do with the way the haplotype can be expressed in a few different ways (as VCF allelic primitives).
We found a back-to-back call of two SNPs that we cannot explain as the BAM file suggests a deletion. IGV screenshot: https://www.dropbox.com/s/c0wfelxc1cca14b/igv_snapshot.png?dl=0
Happy to provide a BAM file, gVCFs etc. But maybe this is easy enough to explain; I just cannot figure out why the joint call for this locus comes out as follows:
The corresponding gVCF block from the sample carrying the complex mutation:
The gVCFs were called with DeepVariant 1.0 - and the per-sample VCFs from that same process show the variant correctly.
GLNexus version: 1.3.1 (docker) DeepVariant version: 1.0 (docker)
GLNexus call: