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Asterisk in the alt feild of VCF?
I have output from the GATK pipeline that includes an asterisk "*" in the alternate allele field at some positions in the VCF file.
chr1 801995 . G A,* 9566.82 PASS AC=7,5;AF=0.438,0.313;AN=16;BaseQRankSum=0.579;DP=521;FS=0.000;MLEAC=7,5;MLEAF=0.438,0.313;MQ=39.56;MQRankSum=0.676;QD=28.82;ReadPosRankSum=1.64;SOR=0.683;VQSLOD=2.30;culprit=ReadPosRankSum GT:AD:DP:GQ:PGT:PID:PL ./.:37,0,0:37 0/1:23,37,0:.:99:1|0:801943_C_T:1217,0,849,1286,960,2246 ./.:18,0,0:18 2/2:0,0,40:.:99:1|1:801943_C_T:1377,1377,1377,120,120,0 ./.:63,0,0:63 0/2:2,0,37:.:99:0|1:801943_C_T:1168,1174,1426,0,252,141 1/1:0,26,0:.:80:1|1:801943_C_T:924,80,0,924,80,924 ./.:31,0,0:31 0/1:3,16,0:.:31:.:.:368,0,31,376,78,455 2/2:1,0,44:.:55:1|1:801943_C_T:1361,1364,1443,55,135,0 0/1:11,27,0:.:99:0|1:801995_G_A:903,0,279,936,360,1295 ./.:36,0,0:36 1/1:1,64,0:.:99:1|1:801995_G_A:2271,175,0,2274,191,2290
What does this asterisk mean?