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ALT * no deletion

fansfans Member
edited October 2018 in Ask the GATK team

my vcf, there is a "*", but I can't find the deletion in OF2-M bam by IGV 。I can't understand why ?
GATK is 3.7 version。Haplotyper --emit_mode gvcf + GVCFtyper
genome is not human.
Thank you!

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  OF1-M   OF2-M   OF3-M   OF4-M   OM1-M   OM2-M   OM3-M   OM4-M
chr3    3619228 .       G       A,*     624.28  .       AC=1,1;AF=0.071,0.071;AN=14;BaseQRankSum=1.514;ClippingRankSum=0.000;DP=211;ExcessHet=3.3579;FS=2.114;MLEAC=1,1;MLEAF=0.071,0.071;MQ=43.88;MQRankSum=0.000;QD=9.18;ReadPosRankSum=0.103;SOR=1.077    GT:AD:DP:GQ:PGT:PID:PL  0/0:21,0,0:21:60:.:.:0,60,771,60,771,771        **0/2:18,0,5:23:99:0|1:3619156_C_A:157,211,967,0,756,740**  0/0:24,0,0:24:66:.:.:0,66,990,66,990,990     0/0:27,0,0:27:81:.:.:0,81,873,81,873,873        0/0:27,0,0:27:81:.:.:0,81,749,81,749,749        0/1:25,20,0:45:99:0|1:3619228_G_A:505,0,588,579,648,1227        0/0:26,0,0:26:36:.:.:0,36,779,36,779,779     ./.:17,0,0:17:.:.:.:.
SNP_Filter=-e 'QUAL<30 || QD<2.0 || FS>60.0 || SOR>4.0 || MQ<40.0 || MQRankSum<-12.5 || ReadPosRankSum<-8.0'
chr3    3619287 .       CCG     C,*     1215.79 PASS    AC=2,1;AF=0.125,0.062;AN=16;BaseQRankSum=0.691;ClippingRankSum=0;DP=211;ExcessHet=0.4576;FS=1.097;MLEAC=2,1;MLEAF=0.125,0.062;MQ=45.88;MQRankSum=0;QD=22.51;ReadPosRankSum=0.785;SOR=0.793   GT:AD:DP:GQ:PGT:PID:PL  0/0:22,0,0:22:63:.:.:0,63,671,63,671,671        **0/2:18,0,5:23:99:0|1:3619156_C_A:157,211,967,0,756,740**  0/0:28,0,0:28:81:.:.:0,81,1215,81,1215,1215  0/0:26,0,0:26:75:.:.:0,75,1125,75,1125,1125     0/0:31,0,0:31:90:.:.:0,90,1350,90,1350,1350     1/1:1,30,0:31:41:1|1:3619228_G_A:1117,41,0,1120,93,1172 0/0:30,0,0:30:84:.:.:0,84,1260,84,1260,1260  0/0:17,0,0:17:51:.:.:0,51,462,51,462,462

chr3 3619228

chr3 3619287

Post edited by shlee on

Best Answer


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