Bcftools filter error

Question

[BAGeno]

Hi,

I am using bcftools filter. I run bcftools filter command in two different ways. It gave me different results.

Command #1

 bcftools filter --e "GQ<20" miss.GT.vcf.gz>test1.vcf

This gave me 49336 variants.

while when I run command 2

 bcftools filter -i "GQ>20" miss.GT.vcf.gz>test2.vcf

It gave me 80858 variants.

There are 80858 variants in original file.

Why there is such variation? Which command results should I consider for further analysis?

[John Marshall]

This may be the recently fixed bcftools issue #1266.

[Pierre Lindenbaum]

what is the version of bcftools ? how is defined GQ in the header ? It's a FORMAT annotation ? with a multi-sample VCF ? show us a few lines with '-i' and '-e'

[BAGeno]

Yes it is multi-sample vcf and GQ field is in FORMAT column.

Here are lines of -e option.

chr1    3787134 rs41307854  A   G   1543.55 PASS    AC=5;AF=0.167;AN=30;BaseQRankSum=-0.367;DB;DP=342;ExcessHet=4.7216;FS=0.688;InbreedingCoeff=-0.2;MLEAC=5;MLEAF=0.167;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=12.65;ReadPosRankSum=-0.152;SOR=0.593;VQSLOD=14.14;culprit=MQRankSum  GT:AD:DP:GQ:PL  0/0:40,0:40:99:0,99,1485    0/0:27,0:27:62:0,62,956 0/0:23,0:23:69:0,69,844 0/0:14,0:14:39:0,39,585 0/0:15,0:15:42:0,42,630 0/0:15,0:15:36:0,36,540 0/1:11,6:17:99:151,0,370    0/0:25,0:25:72:0,72,731 0/1:16,10:26:99:232,0,456   0/0:24,0:24:52:0,52,837 0/0:14,0:14:36:0,36,540 0/0:20,0:20:57:0,57,855 0/1:3,9:12:54:278,0,54  0/1:20,21:41:99:556,0,686   0/1:13,13:26:99:387,0,420
chr1    3787146 rs2253143   G   A   284.27  PASS    AC=1;AF=0.033;AN=30;BaseQRankSum=-0.261;DB;DP=406;ExcessHet=3.0103;FS=0;InbreedingCoeff=-0.0346;MLEAC=1;MLEAF=0.033;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=10.53;ReadPosRankSum=1.2;SOR=0.804;VQSLOD=14.49;culprit=MQRankSum  GT:AD:DP:GQ:PL  0/0:40,0:40:99:0,99,1485    0/0:29,0:29:81:0,81,1215    0/0:30,0:30:90:0,90,995 0/0:19,0:19:54:0,54,810 0/1:13,14:27:99:320,0,274   0/0:15,0:15:42:0,42,630 0/0:21,0:21:54:0,54,810 0/0:27,0:27:81:0,81,775 0/0:39,0:39:99:0,99,1485    0/0:32,0:32:93:0,93,1395    0/0:17,0:17:51:0,51,559 0/0:23,0:23:26:0,26,699 0/0:15,0:15:39:0,39,585 0/0:42,0:42:99:0,102,1530   0/0:29,0:29:84:0,84,1260
chr1    3815401 rs12728401  G   A   487.67  PASS    AC=2;AF=0.067;AN=30;BaseQRankSum=2.62;DB;DP=403;ExcessHet=3.1627;FS=2.28;InbreedingCoeff=-0.0715;MLEAC=2;MLEAF=0.067;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=7.87;ReadPosRankSum=0.946;SOR=0.411;VQSLOD=13.61;culprit=MQRankSum    GT:AD:DP:GQ:PL  0/0:41,0:41:99:0,99,1485    0/0:40,0:40:99:0,102,1530   0/0:21,0:21:63:0,63,548 0/1:24,10:34:99:216,0,524   0/0:33,0:33:93:0,93,1395    0/0:21,0:21:60:0,60,713 0/0:14,0:14:36:0,36,540 0/0:26,0:26:29:0,29,642 0/0:18,0:18:45:0,45,675 0/0:21,0:21:57:0,57,855 0/1:17,11:28:99:316,0,383   0/0:22,0:22:48:0,48,720 0/0:22,0:22:60:0,60,900 0/0:41,0:41:99:0,99,1485    0/0:21,0:21:60:0,60,835

Here are lines of -i option

chr1    215578972   rs41303271  T   C   794.07  PASS    AC=3;AF=0.1;AN=30;BaseQRankSum=-0.229;DB;DP=210;ExcessHet=3.4845;FS=1.01;InbreedingCoeff=-0.1139;MLEAC=3;MLEAF=0.1;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=14.18;ReadPosRankSum=0.561;SOR=0.544;VQSLOD=14.34;culprit=MQRankSum GT:AD:DP:GQ:PL  0/0:6,0:6:18:0,18,227   0/0:9,0:9:27:0,27,279   0/0:20,0:20:60:0,60,696 0/1:10,7:17:99:203,0,301    0/0:24,0:24:66:0,66,990 0/1:6,8:14:99:212,0,163 0/0:11,0:11:30:0,30,450 0/1:10,15:25:99:430,0,290   0/0:19,0:19:57:0,57,725 0/0:20,0:20:60:0,60,754 0/0:6,0:6:15:0,15,225   0/0:10,0:10:30:0,30,355 0/0:6,0:6:18:0,18,225   0/0:13,0:13:39:0,39,387 0/0:10,0:10:30:0,30,369
chr1    215620492   rs14137 G   A   10213.3 PASS    AC=10;AF=0.333;AN=30;BaseQRankSum=-0.074;DB;DP=808;ExcessHet=0.3155;FS=0;InbreedingCoeff=0.4;MLEAC=10;MLEAF=0.333;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=18.88;ReadPosRankSum=0.886;SOR=0.684;VQSLOD=14.69;culprit=MQRankSum  GT:AD:DP:GQ:PGT:PID:PL  0/0:41,0:41:99:.:.:0,99,1485    0/0:35,0:35:99:.:.:0,99,1383    1/1:0,101:101:99:.:.:3201,303,0 0/0:39,0:39:99:.:.:0,99,1485    0/1:74,60:134:99:.:.:1507,0,1946    0/0:33,0:33:99:.:.:0,99,1286    0/0:14,0:14:39:.:.:0,39,585 0/1:58,66:124:99:.:.:1801,0,1518    0/1:38,49:87:99:.:.:1366,0,957  0/0:44,0:44:99:.:.:0,99,1485    0/1:21,16:37:99:1|0:215620491_C_T:461,0,597 1/1:0,22:22:66:.:.:843,66,0 0/0:26,0:26:60:.:.:0,60,900 0/0:35,0:35:99:.:.:0,99,1485    1/1:2,34:36:59:.:.:1121,59,0
chr1    215620513   rs3767253   T   C   74.27   PASS    AC=1;AF=0.033;AN=30;BaseQRankSum=-1.349;DB;DP=583;ExcessHet=3.0103;FS=0;InbreedingCoeff=-0.0345;MLEAC=1;MLEAF=0.033;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=6.75;ReadPosRankSum=0.258;SOR=0.527;VQSLOD=14.46;culprit=MQRankSum GT:AD:DP:GQ:PL  0/0:41,0:41:99:0,99,1485    0/0:35,0:35:99:0,99,1383    0/0:67,0:67:99:0,99,1485    0/0:39,0:39:99:0,99,1485    0/0:53,0:53:99:0,99,1485    0/0:39,0:39:99:0,99,1485    0/1:6,5:11:99:110,0,194 0/0:53,0:53:99:0,99,1485    0/0:66,0:66:99:0,120,1800   0/0:44,0:44:99:0,99,1485    0/0:30,0:30:81:0,81,1215    0/0:20,0:20:48:0,48,720 0/0:23,0:23:60:0,60,889 0/0:35,0:35:99:0,99,1485    0/0:27,0:27:72:0,72,1080
chr1    215625732   rs7531580   T   G   296.27  PASS    AC=1;AF=0.033;AN=30;BaseQRankSum=0.892;DB;DP=517;ExcessHet=3.0103;FS=6.021;InbreedingCoeff=-0.0345;MLEAC=1;MLEAF=0.033;MQ=60;MQRankSum=0;POSITIVE_TRAIN_SITE;QD=18.52;ReadPosRankSum=-0.384;SOR=0.078;VQSLOD=13.65;culprit=MQRankSum    GT:AD:DP:GQ:PL  0/0:44,0:44:99:0,114,1710   0/0:32,0:32:90:0,90,1261    0/0:47,0:47:99:0,114,1710   0/0:47,0:47:99:0,102,1595   0/0:48,0:48:99:0,114,1710   0/0:21,0:21:51:0,51,765 0/1:6,10:16:99:332,0,193    0/0:57,0:57:99:0,120,1800   0/0:53,0:53:99:0,120,1800   0/0:53,0:53:99:0,105,1575   0/0:17,0:17:45:0,45,675 0/0:23,0:23:30:0,30,721 0/0:16,0:16:33:0,33,495 0/0:29,0:29:81:0,81,1215    0/0:14,0:14:36:0,36,540

[Pierre Lindenbaum]

see John Marshall 's answer. Check your version of bcftools.

Answer 1

[BAGeno]

I am using bcftools 1.9. Do I need to install latest version?