VCF file SNP ID missing
REQUIRED for all errors and issues:
a) GATK version used: GATK 4.3.0
b) Exact command used: I used the command stated on gatk4.3.0 without any modifications and I combine and genotyped my vcf files. When I check the VCF file after haplotype caller, combing and genotyping of all vcf files, the SNP ID for all samples in all CHROM was missing and indicated by '.' I try to use variant annotator still, it doesn't work for me. I would appreciate if you share me your experience to solve such problem.
-
Did you use the --dbsnp parameter of the HaplotypeCaller? Those IDs come from a feature file
--dbsnp,-D <FeatureInput> dbSNP file Default value: null.
-
Hello SkyWarrior,
When I run BQSR, I used dbSNPs while during HaplotypeCaller I did not use --dbSNP option. Now, I use -D dbSNP when I try to combine individual VCF files and still the ID part is missing. The vcf file has CHRO number and Position. Would you please suggest me a solution to continue my analysis.
Thank you!
-
You need to provide a dbsnp.vcf file with that parameter therefore HaplotypeCaller can pull ID information from that resource file directly.
-
So what shall I do now? I do have 150 samples and it takes more than 6 month. Is there any way to solve at this stage?
-
Am I suppose to repeat the haplotype caller stage again?
-
You can use VariantAnnotator to add rsIDs to vcfs directly.
-
Could you please send me the full command and suggest me by what tool am I going to annotate it? I am quite new for Bioinformatics. Thank you so much!
-
I used this "gatk VariantAnnotator -R reference.fasta -V input.vcf -O output.vcf --dbsnp dbSNP.vcf". Still, the problem is existing in my vcf file.
-
Is your dbsnp.vcf file compatible with your reference genome. I just tried the below command and here is the result
Before annotation
chr1 10439 . AC A 184.6 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.537;DP=24;ExcessHet=0;FS=1.952;MLEAC=1;MLEAF=0.5;MQ=43.38;MQRankSum=-0.804;QD=10.26;ReadPosRankSum=2.1;SOR=1.329 GT:AD:DP:GQ:PL 0/1:10,8:18:99:192,0,310
chr1 10468 . TCGCGG T 54.6 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.817;DP=21;ExcessHet=0;FS=0;MLEAC=1;MLEAF=0.5;MQ=45.04;MQRankSum=-0.379;QD=4.2;ReadPosRankSum=-2.423;SOR=1.508 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:9,4:13:62:0|1:10468_TCGCGG_T:62,0,368:10468
chr1 10474 . T A 52.64 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.42;DP=14;ExcessHet=0;FS=0;MLEAC=1;MLEAF=0.5;MQ=46.46;MQRankSum=-0.379;QD=4.05;ReadPosRankSum=-3.195;SOR=1.508 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:9,4:13:60:0|1:10468_TCGCGG_T:60,0,369:10468
chr1 13813 . T G 145.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-3.504;DP=33;ExcessHet=0;FS=5.217;MLEAC=1;MLEAF=0.5;MQ=28.19;MQRankSum=-3.147;QD=4.41;ReadPosRankSum=-0.398;SOR=2.093 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:27,6:33:99:0|1:13813_T_G:153,0,1087:13813
chr1 13838 . C T 127.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-0.636;DP=39;ExcessHet=0;FS=2.491;MLEAC=1;MLEAF=0.5;MQ=28.83;MQRankSum=-3.167;QD=3.27;ReadPosRankSum=0;SOR=1.402 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:33,6:39:99:0|1:13813_T_G:135,0,1224:13813
chr1 13868 . A G 161.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-1.098;DP=26;ExcessHet=0;FS=0;MLEAC=1;MLEAF=0.5;MQ=31.24;MQRankSum=-0.226;QD=6.22;ReadPosRankSum=1.37;SOR=1.022 GT:AD:DP:GQ:PL 0/1:18,8:26:99:169,0,447
chr1 14464 . A T 349.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-1.572;DP=70;ExcessHet=0;FS=4.136;MLEAC=1;MLEAF=0.5;MQ=35.71;MQRankSum=1.04;QD=5.3;ReadPosRankSum=1.96;SOR=1.292 GT:AD:DP:GQ:PL 0/1:50,16:66:99:357,0,1491
chr1 14599 . T A 115.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-2.225;DP=49;ExcessHet=0;FS=7.854;MLEAC=1;MLEAF=0.5;MQ=29.54;MQRankSum=-4.059;QD=2.36;ReadPosRankSum=1.88;SOR=2.584 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:43,6:49:99:0|1:14599_T_A:123,0,1769:14599
chr1 14604 . A G 112.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=1.72;DP=50;ExcessHet=0;FS=7.773;MLEAC=1;MLEAF=0.5;MQ=29.96;MQRankSum=-4.054;QD=2.25;ReadPosRankSum=1.24;SOR=2.524 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:44,6:50:99:0|1:14599_T_A:120,0,1805:14599
chr1 14610 . T C 111.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=1.63;DP=56;ExcessHet=0;FS=7.954;MLEAC=1;MLEAF=0.5;MQ=29.95;MQRankSum=-4.147;QD=2.23;ReadPosRankSum=1.12;SOR=2.704 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:44,6:50:99:0|1:14599_T_A:119,0,1813:14599
chr1 14653 . C T 231.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=3.15;DP=67;ExcessHet=0;FS=8.016;MLEAC=1;MLEAF=0.5;MQ=28.92;MQRankSum=-5.231;QD=3.51;ReadPosRankSum=-3.68;SOR=1.786 GT:AD:DP:GQ:PL 0/1:50,16:66:99:239,0,1232
chr1 15274 . A G 228.04 Failed_HC_Filter AC=2;AF=1;AN=2;DP=10;ExcessHet=0;FS=0;MLEAC=2;MLEAF=1;MQ=30.09;QD=28.5;SOR=1.863 GT:AD:DP:GQ:PL 1/1:0,8:8:24:242,24,0
chr1 15820 . G T 293.64 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.56;DP=24;ExcessHet=0;FS=11.563;MLEAC=1;MLEAF=0.5;MQ=44.44;MQRankSum=1.09;QD=14.68;ReadPosRankSum=0.991;SOR=1.989 GT:AD:DP:GQ:PL 0/1:11,9:20:99:301,0,299
chr1 15903 . G GC 164.6 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.7;DP=25;ExcessHet=0;FS=12.852;MLEAC=1;MLEAF=0.5;MQ=49.79;MQRankSum=-3.031;QD=6.86;ReadPosRankSum=-0.1;SOR=3.912 GT:AD:DP:GQ:PL 0/1:18,6:24:99:172,0,644
chr1 16298 . C T 116.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=2.83;DP=94;ExcessHet=0;FS=1.214;MLEAC=1;MLEAF=0.5;MQ=45.64;MQRankSum=-5.337;QD=1.27;ReadPosRankSum=2.46;SOR=0.965 GT:AD:DP:GQ:PL 0/1:80,12:92:99:124,0,2320
chr1 16378 . T C 49.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-3.217;DP=71;ExcessHet=0;FS=5.323;MLEAC=1;MLEAF=0.5;MQ=40.33;MQRankSum=-3.063;QD=0.72;ReadPosRankSum=-1.49;SOR=1.319 GT:AD:DP:GQ:PL 0/1:60,9:69:57:57,0,1771
chr1 16495 . G C 401.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-1.657;DP=86;ExcessHet=0;FS=14.746;MLEAC=1;MLEAF=0.5;MQ=32.35;MQRankSum=-3.048;QD=4.73;ReadPosRankSum=1.7;SOR=1.509 GT:AD:DP:GQ:PL 0/1:60,25:85:99:409,0,1542
chr1 16949 . A C 225.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=0.038;DP=62;ExcessHet=0;FS=2.578;MLEAC=1;MLEAF=0.5;MQ=24.63;MQRankSum=-1.929;QD=4.03;ReadPosRankSum=0.083;SOR=1.082 GT:AD:DP:GQ:PL 0/1:41,15:56:99:233,0,958
chr1 17020 . G A 243.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-0.154;DP=70;ExcessHet=0;FS=10.431;MLEAC=1;MLEAF=0.5;MQ=24.97;MQRankSum=-1.82;QD=3.48;ReadPosRankSum=0.199;SOR=1.2 GT:AD:DP:GQ:PL 0/1:53,17:70:99:251,0,1333
chr1 17385 . G A 181.64 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.35;DP=70;ExcessHet=0;FS=1.193;MLEAC=1;MLEAF=0.5;MQ=40.35;MQRankSum=-1.049;QD=2.67;ReadPosRankSum=-0.475;SOR=0.507 GT:AD:DP:GQ:PL 0/1:56,12:68:99:189,0,1570
chr1 17614 . G A 143.64 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.36;DP=46;ExcessHet=0;FS=1.819;MLEAC=1;MLEAF=0.5;MQ=41.28;MQRankSum=-0.364;QD=3.12;ReadPosRankSum=0.453;SOR=1.195 GT:AD:DP:GQ:PL 0/1:38,8:46:99:151,0,1134
chr1 17722 . A G 41.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-3.002;DP=39;ExcessHet=0;FS=0;MLEAC=1;MLEAF=0.5;MQ=38.78;MQRankSum=0.747;QD=1.07;ReadPosRankSum=-0.996;SOR=0.019 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:35,4:39:49:0|1:17722_A_G:49,0,1437:17722
chr1 17730 . C A 39.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=1.7;DP=42;ExcessHet=0;FS=0;MLEAC=1;MLEAF=0.5;MQ=39.06;MQRankSum=0.642;QD=0.99;ReadPosRankSum=0.035;SOR=0.018 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:36,4:40:47:0|1:17722_A_G:47,0,1446:17722
chr1 19004 . A G 119.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-3.067;DP=11;ExcessHet=0;FS=0;MLEAC=1;MLEAF=0.5;MQ=22.46;MQRankSum=-2.429;QD=10.88;ReadPosRankSum=1.18;SOR=0.859 GT:AD:DP:GQ:PL 0/1:5,6:11:99:127,0,106
chr1 19226 . T A 34.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=0.035;DP=31;ExcessHet=0;FS=9.947;MLEAC=1;MLEAF=0.5;MQ=25.2;MQRankSum=-0.387;QD=1.12;ReadPosRankSum=-1.453;SOR=2.808 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:28,3:31:42:0|1:19226_T_A:42,0,1146:19226
chr1 19249 . G A 142.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=1.53;DP=40;ExcessHet=0;FS=10.715;MLEAC=1;MLEAF=0.5;MQ=24.88;MQRankSum=-0.387;QD=3.57;ReadPosRankSum=-0.834;SOR=2.252 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:34,6:40:99:0|1:19226_T_A:150,0,1410:19226
chr1 19254 . G C 145.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-3.062;DP=39;ExcessHet=0;FS=10.387;MLEAC=1;MLEAF=0.5;MQ=24.95;MQRankSum=-0.438;QD=3.73;ReadPosRankSum=-0.449;SOR=2.258 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:33,6:39:99:0|1:19226_T_A:153,0,1368:19226
chr1 19279 . C T 148.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-0.772;DP=38;ExcessHet=0;FS=10.818;MLEAC=1;MLEAF=0.5;MQ=25;MQRankSum=-0.492;QD=3.91;ReadPosRankSum=1.67;SOR=2.25 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:32,6:38:99:0|1:19226_T_A:156,0,1305:19226
chr1 19355 . G A 83.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-1.219;DP=23;ExcessHet=0;FS=1.804;MLEAC=1;MLEAF=0.5;MQ=24.42;MQRankSum=-1.036;QD=3.64;ReadPosRankSum=-0.847;SOR=1.179 GT:AD:DP:GQ:PL 0/1:17,6:23:91:91,0,466
chr1 19506 . T C 34.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=2;DP=13;ExcessHet=0;FS=11.139;MLEAC=1;MLEAF=0.5;MQ=23.35;MQRankSum=-1.373;QD=2.66;ReadPosRankSum=0.2;SOR=2.207 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:11,2:13:42:0|1:19506_T_C:42,0,431:19506
chr1 19506 . TCC CCG 0 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=2;DP=13;ExcessHet=0;FS=11.13After annotation
chr1 10439 rs112766696 AC A 184.6 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.537;DB;DP=24;ExcessHet=0;FS=1.952;MLEAC=1;MLEAF=0.5;MQ=43.38;MQRankSum=-0.804;QD=10.26;ReadPosRankSum=2.1;SOR=1.329 GT:AD:DP:GQ:PL 0/1:10,8:18:99:192,0,310
chr1 10468 . TCGCGG T 54.6 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.817;DP=21;ExcessHet=0;FS=0;MLEAC=1;MLEAF=0.5;MQ=45.04;MQRankSum=-0.379;QD=4.2;ReadPosRankSum=-2.423;SOR=1.508 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:9,4:13:62:0|1:10468_TCGCGG_T:62,0,368:10468
chr1 10474 . T A 52.64 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.42;DP=14;ExcessHet=0;FS=0;MLEAC=1;MLEAF=0.5;MQ=46.46;MQRankSum=-0.379;QD=4.05;ReadPosRankSum=-3.195;SOR=1.508 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:9,4:13:60:0|1:10468_TCGCGG_T:60,0,369:10468
chr1 13813 . T G 145.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-3.504;DP=33;ExcessHet=0;FS=5.217;MLEAC=1;MLEAF=0.5;MQ=28.19;MQRankSum=-3.147;QD=4.41;ReadPosRankSum=-0.398;SOR=2.093 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:27,6:33:99:0|1:13813_T_G:153,0,1087:13813
chr1 13838 rs28428499 C T 127.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-0.636;DB;DP=39;ExcessHet=0;FS=2.491;MLEAC=1;MLEAF=0.5;MQ=28.83;MQRankSum=-3.167;QD=3.27;ReadPosRankSum=0;SOR=1.402 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:33,6:39:99:0|1:13813_T_G:135,0,1224:13813
chr1 13868 rs796086906 A G 161.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-1.098;DB;DP=26;ExcessHet=0;FS=0;MLEAC=1;MLEAF=0.5;MQ=31.24;MQRankSum=-0.226;QD=6.22;ReadPosRankSum=1.37;SOR=1.022 GT:AD:DP:GQ:PL 0/1:18,8:26:99:169,0,447
chr1 14464 rs546169444 A T 349.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-1.572;DB;DP=70;ExcessHet=0;FS=4.136;MLEAC=1;MLEAF=0.5;MQ=35.71;MQRankSum=1.04;QD=5.3;ReadPosRankSum=1.96;SOR=1.292 GT:AD:DP:GQ:PL 0/1:50,16:66:99:357,0,1491
chr1 14599 rs707680 T A 115.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-2.225;DB;DP=49;ExcessHet=0;FS=7.854;MLEAC=1;MLEAF=0.5;MQ=29.54;MQRankSum=-4.059;QD=2.36;ReadPosRankSum=1.88;SOR=2.584 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:43,6:49:99:0|1:14599_T_A:123,0,1769:14599
chr1 14604 rs541940975 A G 112.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=1.72;DB;DP=50;ExcessHet=0;FS=7.773;MLEAC=1;MLEAF=0.5;MQ=29.96;MQRankSum=-4.054;QD=2.25;ReadPosRankSum=1.24;SOR=2.524 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:44,6:50:99:0|1:14599_T_A:120,0,1805:14599
chr1 14610 rs878986575 T C 111.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=1.63;DB;DP=56;ExcessHet=0;FS=7.954;MLEAC=1;MLEAF=0.5;MQ=29.95;MQRankSum=-4.147;QD=2.23;ReadPosRankSum=1.12;SOR=2.704 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:44,6:50:99:0|1:14599_T_A:119,0,1813:14599
chr1 14653 rs62635297 C T 231.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=3.15;DB;DP=67;ExcessHet=0;FS=8.016;MLEAC=1;MLEAF=0.5;MQ=28.92;MQRankSum=-5.231;QD=3.51;ReadPosRankSum=-3.68;SOR=1.786 GT:AD:DP:GQ:PL 0/1:50,16:66:99:239,0,1232
chr1 15274 rs2758118 A G 228.04 Failed_HC_Filter AC=2;AF=1;AN=2;DB;DP=10;ExcessHet=0;FS=0;MLEAC=2;MLEAF=1;MQ=30.09;QD=28.5;SOR=1.863 GT:AD:DP:GQ:PL 1/1:0,8:8:24:242,24,0
chr1 15820 rs2691315 G T 293.64 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.56;DB;DP=24;ExcessHet=0;FS=11.563;MLEAC=1;MLEAF=0.5;MQ=44.44;MQRankSum=1.09;QD=14.68;ReadPosRankSum=0.991;SOR=1.989 GT:AD:DP:GQ:PL 0/1:11,9:20:99:301,0,299
chr1 15903 rs557514207 G GC 164.6 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.7;DB;DP=25;ExcessHet=0;FS=12.852;MLEAC=1;MLEAF=0.5;MQ=49.79;MQRankSum=-3.031;QD=6.86;ReadPosRankSum=-0.1;SOR=3.912 GT:AD:DP:GQ:PL 0/1:18,6:24:99:172,0,644
chr1 16298 rs2747966 C T 116.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=2.83;DB;DP=94;ExcessHet=0;FS=1.214;MLEAC=1;MLEAF=0.5;MQ=45.64;MQRankSum=-5.337;QD=1.27;ReadPosRankSum=2.46;SOR=0.965 GT:AD:DP:GQ:PL 0/1:80,12:92:99:124,0,2320
chr1 16378 rs148220436 T C 49.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-3.217;DB;DP=71;ExcessHet=0;FS=5.323;MLEAC=1;MLEAF=0.5;MQ=40.33;MQRankSum=-3.063;QD=0.72;ReadPosRankSum=-1.49;SOR=1.319 GT:AD:DP:GQ:PL 0/1:60,9:69:57:57,0,1771
chr1 16495 rs3210724 G C 401.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-1.657;DB;DP=86;ExcessHet=0;FS=14.746;MLEAC=1;MLEAF=0.5;MQ=32.35;MQRankSum=-3.048;QD=4.73;ReadPosRankSum=1.7;SOR=1.509 GT:AD:DP:GQ:PL 0/1:60,25:85:99:409,0,1542
chr1 16949 rs199745162 A C 225.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=0.038;DB;DP=62;ExcessHet=0;FS=2.578;MLEAC=1;MLEAF=0.5;MQ=24.63;MQRankSum=-1.929;QD=4.03;ReadPosRankSum=0.083;SOR=1.082 GT:AD:DP:GQ:PL 0/1:41,15:56:99:233,0,958
chr1 17020 rs199740902 G A 243.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-0.154;DB;DP=70;ExcessHet=0;FS=10.431;MLEAC=1;MLEAF=0.5;MQ=24.97;MQRankSum=-1.82;QD=3.48;ReadPosRankSum=0.199;SOR=1.2 GT:AD:DP:GQ:PL 0/1:53,17:70:99:251,0,1333
chr1 17385 rs201535981 G A 181.64 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.35;DB;DP=70;ExcessHet=0;FS=1.193;MLEAC=1;MLEAF=0.5;MQ=40.35;MQRankSum=-1.049;QD=2.67;ReadPosRankSum=-0.475;SOR=0.507 GT:AD:DP:GQ:PL 0/1:56,12:68:99:189,0,1570
chr1 17614 rs201057270 G A 143.64 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=2.36;DB;DP=46;ExcessHet=0;FS=1.819;MLEAC=1;MLEAF=0.5;MQ=41.28;MQRankSum=-0.364;QD=3.12;ReadPosRankSum=0.453;SOR=1.195 GT:AD:DP:GQ:PL 0/1:38,8:46:99:151,0,1134
chr1 17722 rs376731495 A G 41.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-3.002;DB;DP=39;ExcessHet=0;FS=0;MLEAC=1;MLEAF=0.5;MQ=38.78;MQRankSum=0.747;QD=1.07;ReadPosRankSum=-0.996;SOR=0.019 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:35,4:39:49:0|1:17722_A_G:49,0,1437:17722
chr1 17730 . C A 39.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=1.7;DP=42;ExcessHet=0;FS=0;MLEAC=1;MLEAF=0.5;MQ=39.06;MQRankSum=0.642;QD=0.99;ReadPosRankSum=0.035;SOR=0.018 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:36,4:40:47:0|1:17722_A_G:47,0,1446:17722
chr1 19004 rs62101625 A G 119.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-3.067;DB;DP=11;ExcessHet=0;FS=0;MLEAC=1;MLEAF=0.5;MQ=22.46;MQRankSum=-2.429;QD=10.88;ReadPosRankSum=1.18;SOR=0.859 GT:AD:DP:GQ:PL 0/1:5,6:11:99:127,0,106
chr1 19226 rs62636376 T A 34.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=0.035;DB;DP=31;ExcessHet=0;FS=9.947;MLEAC=1;MLEAF=0.5;MQ=25.2;MQRankSum=-0.387;QD=1.12;ReadPosRankSum=-1.453;SOR=2.808 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:28,3:31:42:0|1:19226_T_A:42,0,1146:19226
chr1 19249 rs879368491 G A 142.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=1.53;DB;DP=40;ExcessHet=0;FS=10.715;MLEAC=1;MLEAF=0.5;MQ=24.88;MQRankSum=-0.387;QD=3.57;ReadPosRankSum=-0.834;SOR=2.252 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:34,6:40:99:0|1:19226_T_A:150,0,1410:19226
chr1 19254 rs879460869 G C 145.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-3.062;DB;DP=39;ExcessHet=0;FS=10.387;MLEAC=1;MLEAF=0.5;MQ=24.95;MQRankSum=-0.438;QD=3.73;ReadPosRankSum=-0.449;SOR=2.258 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:33,6:39:99:0|1:19226_T_A:153,0,1368:19226
chr1 19279 . C T 148.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-0.772;DP=38;ExcessHet=0;FS=10.818;MLEAC=1;MLEAF=0.5;MQ=25;MQRankSum=-0.492;QD=3.91;ReadPosRankSum=1.67;SOR=2.25 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:32,6:38:99:0|1:19226_T_A:156,0,1305:19226
chr1 19355 rs879101641 G A 83.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-1.219;DB;DP=23;ExcessHet=0;FS=1.804;MLEAC=1;MLEAF=0.5;MQ=24.42;MQRankSum=-1.036;QD=3.64;ReadPosRankSum=-0.847;SOR=1.179 GT:AD:DP:GQ:PL 0/1:17,6:23:91:91,0,466
chr1 19506 . T C 34.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=2;DP=13;ExcessHet=0;FS=11.139;MLEAC=1;MLEAF=0.5;MQ=23.35;MQRankSum=-1.373;QD=2.66;ReadPosRankSum=0.2;SOR=2.207 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:11,2:13:42:0|1:19506_T_C:42,0,431:19506
chr1 19506 . TCC CCG 0 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=2;DP=13;ExcessHet=0;FS=11.139;MLEAC=1;MLEAF=0.5;MQ=23.35;MQRankSum=-1.373;QD=2.66;ReadPosRankSum=0.2;SOR=2.207 GT:AD:DP 0|1:43,7:50
chr1 19508 . C G 34.64 Failed_HC_Filter AC=1;AF=0.5;AN=2;BaseQRankSum=-0.224;DP=13;ExcessHet=0;FS=11.139;MLEAC=1;MLEAF=0.5;MQ=23.35;MQRankSum=-1.373;QD=2.66;ReadPosRankSum=-0.545;SOR=2.207 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:11,2:13:42:0|1:19506_T_C:42,0,431:19506
Please sign in to leave a comment.
9 comments