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Denovo detection w/ VariantAnnotator PossibleDeNovo

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    Genevieve Brandt

    Hi Maxime, it does look like this variant should be annotated as a LoConfDeNovo. Could you provide some more information so we can look into it? First, how did you create your VCF? Also, could you send some lines of variants that were annotated as high or low confidence de novo?

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    Maxime

    Hi Mrs Brandt,

     

    I did not create the VCF myself, I got a whole set of it from this study : https://www.nature.com/articles/ng.3303

    I can provide the header if you need.

    Here are some variants annotated as

    - high :

    1 46660555 . CCAGG GCAGA 702.80 . AB=0;ABP=0;AC=1;AF=0.125;AN=8;AO=6;CIGAR=1X3M1X;DP=81;DPB=1517.4;DPRA=1.0416;EFF=NON_SYNONYMOUS_CODING(MODERATE||gccctgggc/gcTCTGCgc|ALG203ALR|660|POMGNT1||CODING|NM_017739.3||1),NON_SYNONYMOUS_CODING(MODERATE||gccctgggc/gcTCTGCgc|ALG203ALR|748|POMGNT1||CODING|NM_001243766.1||1);EPP=16.0391;EPPR=16.4165;GTI=1;LEN=5;MEANALT=4.6;MQM=60;MQMR=59.939;NS=84;NUMALT=1;ODDS=1.76988;PAIRED=1;PAIREDR=0.997713;PAO=1;PQA=2;PQR=2558;PRO=109.5;QA=12;QR=38701;RO=1312;RPP=8.80089;RPPR=84.5795;RUN=1;SAF=1;SAP=8.80089;SAR=5;SRF=624;SRP=9.78953;SRR=688;TYPE=complex;hiConfDeNovo=13534.s1;set=variant;technology.ILLUMINA=1 GT:AO:DP:GQ:PL:QA:QR:RO 0/0:0:24:99:0,64,100:0:621:21 0/0:0:21:99:0,54,100:0:608:20 0/0:0:16:99:0,49,100:0:461:15 0/1:0:20:50:100,0,100:0:471:18

    2 162280578 . GGATT AGATA 735.21 . AB=0;ABP=0;AC=1;AF=0.125;AN=8;AO=6;CIGAR=1X3M1X;DP=40;DPB=681.8;DPRA=1.41273;EFF=NON_SYNONYMOUS_CODING(MODERATE||gggatt/gAGATA|GI630EI|682|TBR1||CODING|NM_006593.2||1);EPP=16.0391;EPPR=9.62488;GTI=0;LEN=5;MEANALT=2;MQM=60;MQMR=59.9061;NS=84;NUMALT=1;ODDS=7.89637;PAIRED=1;PAIREDR=0.998353;PAO=0;PQA=0;PQR=867.5;PRO=43;QA=12;QR=16599;RO=607;RPP=8.80089;RPPR=4.30174;RUN=1;SAF=5;SAP=8.80089;SAR=1;SRF=426;SRP=217.743;SRR=181;TYPE=complex;hiConfDeNovo=13534.s1;set=variant12;technology.ILLUMINA=1 GT:AO:DP:GQ:PL:QA:QR:RO 0/0:0:17:80:0,46,100:0:479:16 0/0:0:3:42:0,8,90:0:96:3 0/0:0:13:75:0,41,100:0:388:13 0/1:0:7:90:100,0,100:0:169:6

    - low : 

    3 47138130 . TGG TGA 146.81 . AB=0;ABP=0;AC=1;AF=0.125;AN=8;AO=4;CIGAR=2M1X;DP=27;DPB=488;DPRA=1.55687;EFF=INTRON(MODIFIER||||2564|SETD2||CODING|NM_014159.6|9|1);EPP=5.18177;EPPR=123.857;GTI=2;LEN=1;MEANALT=1.66667;MQM=60;MQMR=60.0065;NS=82;NUMALT=1;ODDS=3.16554;PAIRED=1;PAIREDR=0.980435;PAO=2.66667;PQA=68.6667;PQR=184.667;PRO=13.6667;QA=17;QR=12924;RO=460;RPP=3.0103;RPPR=117.891;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=364;SRP=342.062;SRR=96;TYPE=snp;loConfDeNovo=13534.p1;set=variant16;technology.ILLUMINA=1 GT:AO:DP:GQ:PL:QA:QR:RO 0/0:0:6:48:0,17,100:0:186:6 0/0:0:9:52:0,21,100:0:249:9 0/1:0:7:17:48,0,100:0:217:7 0/0:0:5:45:0,14,100:0:149:5

    6 33405860 . GCAA GCAG 389.44 . AB=0.2;ABP=6.91895;AC=1;AF=0.125;AN=8;AO=5;CIGAR=3M1X;DP=25;DPB=649.75;DPRA=0.802247;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K394R|1343|SYNGAP1||CODING|NM_006772.2.2|8|1);EPP=6.91895;EPPR=903.043;GTI=4;LEN=1;MEANALT=1.66667;MQM=60;MQMR=59.926;NS=83;NUMALT=1;ODDS=1.10201;PAIRED=1;PAIREDR=0.988487;PAO=0.5;PQA=16;PQR=1007;PRO=59.5;QA=29;QR=17618;RO=608;RPP=3.44459;RPPR=1237.84;RUN=1;SAF=4;SAP=6.91895;SAR=1;SRF=565;SRP=976.187;SRR=43;TYPE=snp;loConfDeNovo=13534.s1;set=variant19;technology.ILLUMINA=1 GT:AO:DP:GQ:PL:QA:QR:RO 0/0:0:8:65:0,25,100:0:241:8 0/0:0:4:52:0,11,100:0:122:4 0/0:0:5:60:0,19,100:0:151:5 0/1:0:8:19:48,0,100:0:241:8

     

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    Genevieve Brandt

    Hi Maxime, for the variant that was not called as lowConfDeNovo but should be, could you send me the entire line from your VCF (including the info line)?

    Also, would you be able to upload some of your files so that we can look into this problem? We wanted to see the pre-annotated VCF and the pedigree file. Here are instructions on how to do that. 

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    Maxime

    Hi, sorry for the delay.

     

    Here is the full line before the denovo analysis, please note that this entier VCF file did not contain a denovo tagged variant after VariantAnnotator :

     

    12 2721137 . C T 41828.1 . AB=0.425684;ABP=157.285;AC=1;AF=0.125;AN=8;AO=2027;CIGAR=1X;DP=117;DPB=10217;DPRA=1.70286;EPP=97.5063;EPPR=574.656;GTI=2;LEN=1;MEANALT=1.27778;MQM=59.6556;MQMR=59.6566;NS=63;NUMALT=1;ODDS=0.903071;PAIRED=0.9852;PAIREDR=0.983242;PAO=0;PQA=0;PQR=0;PRO=0;QA=56942;QR=256675;RO=8175;RPP=14.3754;RPPR=55.6104;RUN=1;SAF=967;SAP=12.2757;SAR=1060;SRF=3645;SRP=211.053;SRR=4530;TYPE=snp;set=variant4;technology.illumina=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1259|2135|CACNA1C||CODING|NM_001129844.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2127|CACNA1C||CODING|NM_001129846.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2138|CACNA1C||CODING|NM_000719.6|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2138|CACNA1C||CODING|NM_001129840.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2138|CACNA1C||CODING|NM_001129841.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2138|CACNA1C||CODING|NM_001129842.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2138|CACNA1C||CODING|NM_001129843.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2138|CACNA1C||CODING|NM_001167623.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2144|CACNA1C||CODING|NM_001129839.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2146|CACNA1C||CODING|NM_001129837.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2146|CACNA1C||CODING|NM_001129838.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2155|CACNA1C||CODING|NM_001129836.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2157|CACNA1C||CODING|NM_001129833.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2157|CACNA1C||CODING|NM_001129834.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2157|CACNA1C||CODING|NM_001129835.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2166|CACNA1C||CODING|NM_001129831.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2173|CACNA1C||CODING|NM_001129830.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2173|CACNA1C||CODING|NM_001167624.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2179|CACNA1C||CODING|NM_001129829.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1262|2198|CACNA1C||CODING|NM_001167625.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1282|2158|CACNA1C||CODING|NM_001129832.1|30|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1282|2186|CACNA1C||CODING|NM_001129827.1|30|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F1282|2221|CACNA1C||CODING|NM_199460.2|30|1);CADD_p=10.35;CADD_score=1.327280 GT:AO:DP:GQ:QA:QR:RO 0/0:0:13:59:0:456:13 0/0:1:3:1:33:81:2 0/1:3:10:54:94:210:7 0/0:0:91:99:0:2777:91

     

    Will upload the pre-annotated and the pedigree file asap.

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    Maxime

    Files should be uploaded on the FTP server, archive name is GATK_report_denovo.zip

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    Genevieve Brandt

    Hi Maxime, thank you for updating me with the VCF line as well of the information that no variants from this VCF were called as low or high confidence deNovo. I think the issue here is with the absence of PL in this VCF. Please see Genotype Refinement workflow for information on how to get the PossibleDeNovo annotation. In that workflow, CalculateGenotypePosteriors is run to get the PL annotation, which is the difference between the low/highConfDenovo VCF lines you shared with me and the VCF that had no annotations.

    Please try this and let me know if it works.

    Note: We have also updated our documentation for PossibleDenovo recently, where you can see that it is important to follow the Genotype Refinement workflow in order to get the PossibleDenovo annotation. 

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