asterisc in some lines of my vcf file

Dear all,

I ran the haplotype caller, in order to find germline variants in my samples (808 samples). But in the ALT column I found "*" in some lines, and I dont know what does it mean.... (I follow the best practices, run gatk, use dbimport to merge the samples and finally I did the VQSR steps. For SNPs I did the genotype posteriors). Here an example:

1 10119 . CT *,C 39.21 . AC=1,2;AF=6.369e-04,1.274e-03;AN=1570;AS_FilterStatus=NA,NA;AS_VQSLOD=NaN,NaN;AS_culprit=NA,NA;BaseQRankSum=0.00;ClippingRankSum=0.00;DP=104112;ExcessHet=3.0186;FS=1.725;InbreedingCoeff=-0.0013;MLEAC=1,1;MLEAF=6.378e-04,6.378e-04;MQ=17.57;MQRankSum=-3.250e-01;PG=0,0,0,0,0,0;QD=1.87;ReadPosRankSum=0.482;SOR=1.127 GT:AD:DP:GQ:PGT:PID:PL:PP 0/0:130,0,0:130:81:.:.:0,81,1215,81,1215,1215:0,81,1215,81,1215,1215 0/1:6,3,0:9:52:.:.:52,0,159,71,168,239:52,0,159,71,168,239 0/0:132,0,0:132:81:.:.:0,81,1215,81,1215,1215:0,81,1215,81,1215,1215

1 66240 . T *,A 16289.75 VQSRTrancheSNP99.90to100.00 AC=80,2;AF=0.051,1.274e-03;AN=1570;AS_FilterStatus=NA,VQSRTrancheSNP99.90to100.00;AS_VQSLOD=NaN,-4.4852;AS_culprit=NA,DP;BaseQRankSum=1.04;ClippingRankSum=0.00;DP=7862;ExcessHet=-0.0000;FS=1.321;InbreedingCoeff=0.3618;MLEAC=123,3;MLEAF=0.107,2.604e-03;MQ=6.93;MQRankSum=-1.151e+00;PG=0,6,18,22,32,49;QD=20.04;ReadPosRankSum=-4.250e-01;SOR=0.841 GT:AD:DP:GQ:PGT:PID:PL:PP 0/0:4,0,0:4:18:.:.:0,12,181,12,181,181:0,18,199,34,213,230 0/0:18,0,0:18:42:.:.:0,36,540,36,540,540:0,42,558,58,572,589

1 66390 . T *,A 7475.63 VQSRTrancheSNP99.00to99.90 AC=36,3;AF=0.023,1.911e-03;AN=1570;AS_FilterStatus=NA,VQSRTrancheSNP99.00to99.90;AS_VQSLOD=NaN,2.9789;AS_culprit=NA,DP;BaseQRankSum=0.180;ClippingRankSum=0.00;DP=10958;ExcessHet=0.0000;FS=7.105;InbreedingCoeff=0.1627;MLEAC=39,3;MLEAF=0.025,1.961e-03;MQ=23.91;MQRankSum=0.00;PG=0,13,32,24,40,53;QD=18.37;ReadPosRankSum=0.119;SOR=0.474 GT:AD:DP:GQ:PGT:PID:PL:PP 0/1:1,9,0:10:34:0|1:66349_TA_T:375,0,15,378,42,420:362,0,34,389,69,460 0/0:12,0,0:12:43:.:.:0,30,450,30,450,450:0,43,482,54,490,503 0/0:1,0,0:1:16:.:.:0,3,27,3,27,27:0,16,59,27,67,80


The vast majority dont accomplish the trances, but why appear *?? this is an example but i have 808 samples.


THanks for your time

Jordi

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