CalculateGenotypePosteriors - supporting file

astrand

Hi,

I used CalculateGenotypePosteriors with the supporting file called ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.vcf, obtained from 1000 Genomes. It contains both indels and SNPs, and I was able to use the file for the first step of the Genotype Refinement Workflow. My question is: is it an issue that I didn't remove the indels from the supporting file? I would presume not since first of all, both the indels and the SNPs from Phase 3 of 1000G should be high confidence, and second, my recalibrated vcf file includes both indels and snps, so it should be in my interest to have as much information as possible, actually, so I should consider indels as well.

Just want to check whether my reasoning is correct.

Thanks,
Alva

Geraldine_VdAuwera

Hi Alva,

It's not a problem at all. Actually the tool only operates on SNPs and does not affect indels.

Geraldine_VdAuwera

Hi Alva,

It's not a problem at all. Actually the tool only operates on SNPs and does not affect indels.

astrand

Great, thanks!

astrand

Hi Geraldine,

I just wanted to follow up on this discussion and note that genotypes belonging to indels seem to have gone through genotype refinement. I thought that indels were not considered by CalculateGenotypePosteriors and VariantFiltration?

Here is an example of an indel that went through this process:

1 20199272 . T TCTTC,C 3520.08 PASS AC=8,22;AF=0.160,0.440;AN=50;BaseQRankSum=-1.356e+00;ClippingRankSum=-1.267e+00;DP=487;FS=4.843;GQ_MEAN=27.84;GQ_STDDEV=40.31;InbreedingCoeff=0.1002;MLEAC=1,12;MLEAF=0.020,0.240;MQ=51.74;MQ0=0;MQRankSum=0.421;NCC=2;PG=0,0,0,0,0,0;QD=32.53;ReadPosRankSum=1.27;SOR=0.699;VQSLOD=0.687;culprit=FS GT:AD:DP:FT:GQ:PGT:PID:PL:PP 2/2:0,0,0:0:PASS:22:.:.:410,207,355,32,22,0:410,207,355,32,22,0 2/2:0,0,1:1:lowGQ:5:.:.:240,51,36,18,5,0:240,51,36,18,5,0 0/2:4,0,4:8:PASS:90:.:.:140,153,256,0,103,90:140,153,256,0,103,90 0/0:22,0,0:22:lowGQ:0:.:.:0,0,390,0,390,390:0,0,390,0,390,390 0/0:2,0,0:2:lowGQ:3:.:.:0,3,45,3,45,45:0,3,45,3,45,45 2/2:0,0,3:3:lowGQ:11:.:.:287,135,124,21,11,0:287,135,124,21,11,0 ./.:7,0,0:7:PASS 2/2:0,0,3:4:lowGQ:11:.:.:282,126,115,22,11,0:282,126,115,22,11,0 0/2:10,0,0:10:lowGQ:5:.:.:27,5,494,0,411,405:27,5,494,0,411,405 0/2:7,0,0:7:lowGQ:13:.:.:13,15,502,0,303,288:13,15,502,0,303,288 0/1:8,6,0:14:PASS:99:.:.:194,0,255,218,273,491:194,0,255,218,273,491 0/0:18,0,0:18:PASS:52:.:.:0,52,755,52,755,755:0,52,755,52,755,755 2/2:0,0,0:0:PASS:23:.:.:305,168,416,23,30,0:305,168,416,23,30,0 0/2:0,0,4:4:lowGQ:14:.:.:40,14,634,0,185,699:40,14,634,0,185,699 0/0:19,0,0:19:PASS:58:.:.:0,58,824,58,824,824:0,58,824,58,824,824 0/0:1,0,0:1:lowGQ:6:0|1:20199257_CT_C:0,6,91,6,91,91:0,6,91,6,91,91 1/1:0,0,0:0:lowGQ:2:.:.:177,11,0,12,2,44:177,11,0,12,2,44 0/1:0,0,3:3:PASS:34:.:.:94,0,388,34,38,304:94,0,388,34,38,304 0/2:15,0,2:17:lowGQ:18:0|1:20199249_CT_C:18,64,695,0,632,624:18,64,695,0,632,624 1/1:0,0,0:0:lowGQ:8:.:.:133,8,0,101,17,265:133,8,0,101,17,265 0/2:3,0,0:3:PASS:25:.:.:129,25,484,0,121,94:129,25,484,0,121,94 0/2:2,0,0:2:PASS:38:.:.:185,38,644,0,88,42:185,38,644,0,88,42 0/2:2,0,0:2:lowGQ:14:.:.:256,14,293,0,57,41:256,14,293,0,57,41./.:11,0,0:11:PASS 1/2:0,0,1:1:lowGQ:14:.:.:115,24,14,36,0,359:115,24,14,36,0,359 1/2:0,0,1:1:PASS:28:.:.:188,39,28,35,0,206:188,39,28,35,0,206 2/2:0,0,3:3:lowGQ:8:1|1:20199249_CT_C:88,88,89,8,9,0:88,88,89,8,9,0

I'm confused as to why some of the genotypes passed when there was no support for their genotype, as is the case for the first genotype: 2/2:0,0,0:0:PASS

Could you clarify this issue for me?

Thanks,
Alva

astrand

The commands I used to generate the refined vcf file were the following:

java -Xmx3g -jar GenomeAnalysisTK.jar -T CalculateGenotypePosteriors -R hs37d5.fa --supporting ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.vcf -ped Hutt.ped -V recalibrated_variants_allHutt_filteredout.vcf -o recalibrated_variants_allHutt.postCGP.f.vcf

java -Xmx3g -jar GenomeAnalysisTK.jar -T VariantFiltration -R hs37d5.fa -V recalibrated_variants_allHutt.postCGP.f.vcf -G_filter "GQ < 20.0" -G_filterName lowGQ -o recalibrated_variants_allHutt.postCGP.Gfiltered.f.vcf

astrand

I was also under the impression that the genotype refinement workflow only operated on biallelic variants - is that correct?

Kurt

The VariantFiltration part doesn't care if it is biallelic or indels or whatever. The reason why it passed is because GQ is 22 (why that is is different story). For the CGP part, did either the genotypes or GQ scores change after CGP from what they were originally for this site?

astrand

No, the genotypes didn't change between applying CalculateGenotypePosteriors and VariantFiltration (between CGP and Gfiltered). It seems like the genotype refinement workflow doesn't filter based on coverage, so a priori I guess I shouldn't expect the genotype to be filtered out. But it's strange that GQ is acceptable for this genotype, in any case.

Geraldine_VdAuwera

@astrand I agree that's a surprising call. Can you please post the details of how you called your variants (including GATK version) as a new question?