What is GenotypeGVCFs?

Question

[wormball]

Hello!

This article https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- says i should use HaplotypeCaller in GVCF mode and GenotypeGVCFs then, and this article https://gatk.broadinstitute.org/hc/en-us/articles/360035531192-RNAseq-short-variant-discovery-SNPs-Indels- advises to use HaplotypeCaller without GenotypeGVCFs. I tried the former (with one sample), and the result is similar to the result of HaplotypeCaller in non-GVCF mode, however it differs in some entries.

What is the difference between these two ways and in which cases should i use one or another? And what GenotypeGVCFs does at all? The manual page says "joint genotyping" but i have no idea what it means.

Thanks in advance.

[Pierre Lindenbaum]

the second article is about RNASeq..

in which cases should i use one or another?

"However, that scaled very poorly with the number of samples, posing unacceptable limits on the size of the study cohorts that could be analyzed in that way. In addition, it was not possible to add samples incrementally to a study; all variant calling work had to be redone when new samples were introduced."

in a nutshell, use GVCF when HaplotypeCaller becomes too slow (=too many samples). I use GVCF when WGS+N_SAMPLES>20.

[wormball]

Thanks! But why are the results are so different between these cases? The variants are mostly the same, but some variants occur in only one case, and also the statistical numbers differ in some variants.

With GenotypeGVCFs:

........
JH584292.1  13158   .   G   A   297.60  .   AC=1;AF=0.500;AN=2;BaseQRankSum=1.49;DP=471;ExcessHet=3.0103;FS=8.334;MLEAC=1;MLEAF=0.500;MQ=55.40;MQRankSum=-9.311e+00;QD=2.24;ReadPosRankSum=-6.472e+00;SOR=2.003 GT:AD:DP:GQ:PGT:PID:PL:PS   0|1:117,16:133:99:0|1:13077_T_G:305,0,5404:13077
JH584292.1  13164   .   C   T   123.60  .   AC=1;AF=0.500;AN=2;BaseQRankSum=3.52;DP=471;ExcessHet=3.0103;FS=3.008;MLEAC=1;MLEAF=0.500;MQ=55.68;MQRankSum=-9.396e+00;QD=0.98;SOR=1.329   GT:AD:DP:GQ:PGT:PID:PL:PS   0|1:115,11:126:99:0|1:13077_T_G:131,0,5500:13077
JH584292.1  13266   .   A   G   2524.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=2.41;DP=250;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=54.56;MQRankSum=0.00;QD=29.36;ReadPosRankSum=4.65;SOR=0.658    GT:AD:DP:GQ:PL  0/1:15,71:86:99:2532,0,258
JH584292.1  14454   .   G   T   3575.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=3.62;DP=546;ExcessHet=3.0103;FS=11.818;MLEAC=1;MLEAF=0.500;MQ=56.23;MQRankSum=3.88;QD=8.35;ReadPosRankSum=-1.564e+00;SOR=0.443  GT:AD:DP:GQ:PL  0/1:288,140:428:99:3583,0,11997
JH584292.1  14457   .   A   T   2031.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=-7.790e-01;DP=528;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.43;MQRankSum=-1.147e+01;QD=4.88;ReadPosRankSum=2.84;SOR=0.762 GT:AD:DP:GQ:PGT:PID:PL:PS   0|1:339,77:416:99:0|1:14457_A_T:2039,0,15261:14457
JH584292.1  14462   .   G   A   2315.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=-5.720e-01;DP=506;ExcessHet=3.0103;FS=14.244;MLEAC=1;MLEAF=0.500;MQ=56.58;MQRankSum=2.81;QD=5.76;ReadPosRankSum=0.830;SOR=1.692 GT:AD:DP:GQ:PGT:PID:PL:PS   0|1:313,89:402:99:0|1:14462_G_A:2323,0,13521:14462
JH584292.1  14472   .   T   G   1878.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=-2.952e+00;DP=456;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.04;MQRankSum=-1.107e+01;QD=5.09;ReadPosRankSum=3.08;SOR=0.685 GT:AD:DP:GQ:PGT:PID:PL:PS   0|1:303,66:369:99:0|1:14457_A_T:1886,0,13939:14457
JH584292.1  14494   .   C   A   1710.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=2.07;DP=383;ExcessHet=3.0103;FS=2.389;MLEAC=1;MLEAF=0.500;MQ=58.33;MQRankSum=-1.161e+01;QD=5.06;ReadPosRankSum=0.615;SOR=0.537  GT:AD:DP:GQ:PGT:PID:PL:PS   0|1:274,64:338:99:0|1:14457_A_T:1718,0,12597:14457
JH584292.1  14498   .   T   A   1528.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=2.95;DP=366;ExcessHet=3.0103;FS=37.019;MLEAC=1;MLEAF=0.500;MQ=58.34;MQRankSum=2.88;QD=4.70;ReadPosRankSum=-9.050e-01;SOR=2.441  GT:AD:DP:GQ:PGT:PID:PL:PS   0|1:268,57:325:99:0|1:14462_G_A:1536,0,12263:14462
...........

Without GenotypeGVCFs:

..............
JH584292.1  13158   .   G   A   106.60  .   AC=1;AF=0.500;AN=2;BaseQRankSum=3.175;DP=532;ExcessHet=3.0103;FS=10.140;MLEAC=1;MLEAF=0.500;MQ=55.89;MQRankSum=-10.738;QD=0.56;ReadPosRankSum=-6.612;SOR=2.040  GT:AD:DP:GQ:PL  0/1:174,16:190:99:114,0,50786
JH584292.1  13226   .   T   TTTGTTCTATCTGAGAGGTCCTG 514.64  .   AC=1;AF=0.500;AN=2;BaseQRankSum=-0.918;DP=692;ExcessHet=3.0103;FS=26.465;MLEAC=1;MLEAF=0.500;MQ=57.97;MQRankSum=1.102;QD=1.51;ReadPosRankSum=-2.181;SOR=1.309   GT:AD:DP:GQ:PL  0/1:290,51:341:99:522,0,11403
JH584292.1  13230   .   T   TTCTATCTGAGAGGTCCTGGTGTGC   1528.64 .   AC=1;AF=0.500;AN=2;BaseQRankSum=-0.512;DP=673;ExcessHet=3.0103;FS=0.640;MLEAC=1;MLEAF=0.500;MQ=57.77;MQRankSum=1.180;QD=6.04;ReadPosRankSum=-4.863;SOR=0.611    GT:AD:DP:GQ:PL  0/1:183,70:253:99:1536,0,8033
JH584292.1  13266   .   A   G   3211.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=3.192;DP=297;ExcessHet=3.0103;FS=10.156;MLEAC=1;MLEAF=0.500;MQ=55.34;MQRankSum=2.592;QD=23.97;ReadPosRankSum=5.815;SOR=0.943    GT:AD:DP:GQ:PL  0/1:42,92:134:99:3219,0,1309
JH584292.1  14167   .   T   A   10396.03    .   AC=2;AF=1.00;AN=2;BaseQRankSum=1.728;DP=336;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.76;MQRankSum=9.661;QD=27.92;ReadPosRankSum=-0.911;SOR=0.424  GT:AD:DP:GQ:PL  1/1:3,278:281:99:10410,795,0
JH584292.1  14196   .   C   G   5723.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=3.501;DP=288;ExcessHet=3.0103;FS=12.561;MLEAC=1;MLEAF=0.500;MQ=59.11;MQRankSum=0.000;QD=24.89;ReadPosRankSum=1.737;SOR=0.647    GT:AD:DP:GQ:PL  0/1:83,147:230:99:5731,0,2634
JH584292.1  14216   .   C   T   6060.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=4.209;DP=257;ExcessHet=3.0103;FS=6.683;MLEAC=1;MLEAF=0.500;MQ=58.41;MQRankSum=0.000;QD=30.46;ReadPosRankSum=4.141;SOR=0.627 GT:AD:DP:GQ:PL  0/1:58,141:199:99:6068,0,1999
JH584292.1  14262   .   G   T   5457.03 .   AC=2;AF=1.00;AN=2;BaseQRankSum=1.887;DP=183;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.34;MQRankSum=9.746;QD=30.62;ReadPosRankSum=1.452;SOR=0.759   GT:AD:DP:GQ:PL  1/1:4,124:128:99:5471,152,0
JH584292.1  14265   .   T   G   5516.03 .   AC=2;AF=1.00;AN=2;BaseQRankSum=1.820;DP=186;ExcessHet=3.0103;FS=2.079;MLEAC=2;MLEAF=1.00;MQ=55.42;MQRankSum=9.861;QD=32.35;ReadPosRankSum=1.465;SOR=0.229   GT:AD:DP:GQ:PL  1/1:4,127:131:99:5530,214,0
JH584292.1  14454   .   G   T   3549.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=3.854;DP=551;ExcessHet=3.0103;FS=10.525;MLEAC=1;MLEAF=0.500;MQ=56.24;MQRankSum=3.897;QD=8.20;ReadPosRankSum=-1.658;SOR=0.371    GT:AD:DP:GQ:PL  0/1:294,139:433:99:3557,0,12262
JH584292.1  14457   .   A   T   2199.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=532;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.44;MQRankSum=-11.394;QD=5.24;ReadPosRankSum=3.087;SOR=0.647   GT:AD:DP:GQ:PL  0/1:339,81:420:99:2207,0,15304
JH584292.1  14462   .   G   A   2310.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=-1.035;DP=512;ExcessHet=3.0103;FS=16.444;MLEAC=1;MLEAF=0.500;MQ=56.60;MQRankSum=2.836;QD=5.66;ReadPosRankSum=0.740;SOR=1.860    GT:AD:DP:GQ:PL  0/1:319,89:408:99:2318,0,13760
JH584292.1  14472   .   T   G   2037.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=-3.056;DP=465;ExcessHet=3.0103;FS=2.262;MLEAC=1;MLEAF=0.500;MQ=57.07;MQRankSum=-10.962;QD=5.39;ReadPosRankSum=3.201;SOR=0.552   GT:AD:DP:GQ:PL  0/1:307,71:378:99:2045,0,14110
JH584292.1  14494   .   C   A   1714.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=2.229;DP=387;ExcessHet=3.0103;FS=1.733;MLEAC=1;MLEAF=0.500;MQ=58.63;MQRankSum=-10.246;QD=5.01;ReadPosRankSum=0.664;SOR=0.562    GT:AD:DP:GQ:PL  0/1:280,62:342:99:1722,0,12824
JH584292.1  14498   .   T   A   1650.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=2.868;DP=372;ExcessHet=3.0103;FS=38.553;MLEAC=1;MLEAF=0.500;MQ=58.62;MQRankSum=2.647;QD=4.99;ReadPosRankSum=-1.242;SOR=2.491    GT:AD:DP:GQ:PL  0/1:271,60:331:99:1658,0,12393
...............