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What do sites labeled "." in FILTER field mean (after running VQSR)?

astrandastrand New YorkMember


After using VQSR, I have a vcf output that contains sites labeled "." in the FILTER field. When I look at the vcf documentation (1000 genomes), it says that those are sites where filters have not been applied. Is this correct? I would like to know more about what these sites mean, exactly.

An example of such a site in my data is:

1 10439 . AC A 4816.02 . AC=10;AF=0.185;AN=54;BaseQRankSum=-4.200e-01;ClippingRankSum=-2.700e-01;DP=1690;FS=6.585;GQ_MEAN=111.04;GQ_STDDEV=147.63;InbreedingCoeff=-0.4596;MLEAC=17;MLEAF=0.315;MQ=36.85;MQ0=0;MQRankSum=-8.340e-01;NCC=0;QD=11.39;ReadPosRankSum=-8.690e-01;SOR=1.226 GT:AD:DP:GQ:PGT:PID:PL 0/1:22,14:36:99:0|1:10439_AC_A:200,0,825 0/0:49,0:49:0:.:.:0,0,533 0/0:92,0:92:0:.:.:0,0,2037 0/1:20,29:49:99:.:.:634,0,340 0/0:11,0:16:32:.:.:0,32,379 0/1:21,17:38:99:.:.:273,0,616 0/0:57,0:57:0:.:.:0,0,1028 0/0:58,0:58:0:.:.:0,0,1204 0/0:52,0:52:0:.:.:0,0,474 0/0:86,0:86:27:.:.:0,27,2537 0/1:13,24:37:99:.:.:596,0,220 0/1:14,34:48:99:.:.:814,0,263 0/0:86,0:86:0:.:.:0,0,865 0/0:61,0:61:0:.:.:0,0,973 0/0:50,0:50:0:.:.:0,0,648 0/0:40,0:40:0:.:.:0,0,666 0/0:79,0:79:0:.:.:0,0,935 0/0:84,0:84:0:.:.:0,0,1252 0/1:22,27:49:99:.:.:618,0,453 0/0:39,0:39:0:.:.:0,0,749 0/0:74,0:74:0:.:.:0,0,1312 0/1:13,18:31:99:.:.:402,0,281 0/0:41,0:44:99:.:.:0,115,1412 0/1:30,9:39:99:.:.:176,0,475 0/1:26,23:49:99:.:.:433,0,550 0/1:13,34:47:99:.:.:736,0,185 0/0:44,0:44:0:.:.:0,0,966



Best Answer


  • astrandastrand New YorkMember

    @pdexheimer, actually, after inspection, I see that there are only "." sites after my first run of VQSR, when applying VQSR on SNPs. I do actually apply this on indels and after I do that, there are no longer any "." sites. Sorry for the confusion, this all makes sense now. Thanks for the help.

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