variant calling by unified genotyper

While using UnifiedGenotyper for variant calling, i am getting the following output. In altered base sometimes instead of single altered base, i am getting three or two different bases. I am unable to understand what does it means. How can i infer the result from this. plz help, i am new to this. Thanks in advance

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT

phytoene_synthase1 980 . C A,G,T 553.14 . AC=2,14,2;AF=0.016,0.109,0.016;AN=128;BaseQRankSum=3.605;DP=250;Dels=0.00;FS=12.534;HaplotypeScore=109.3273;MLEAC=2,14,2;MLEAF=0.016,0.109,0.016;MQ=52.45;MQ0=1;MQRankSum=-7.667;QD=2.21;ReadPosRankSum=-7.988;SOR=2.691 GT:AD:DP:GQ
phytoene_synthase1 981 . A C,G,T 307.38 . AC=3,4,2;AF=0.023,0.031,0.016;AN=128;BaseQRankSum=0.189;DP=250;Dels=0.00;FS=10.700;HaplotypeScore=100.2929;MLEAC=3,4,2;MLEAF=0.023,0.031,0.016;MQ=52.49;MQ0=1;MQRankSum=-4.932;QD=1.23;ReadPosRankSum=-6.447;SOR=2.649 GT:AD:DP:GQ
phytoene_synthase1 982 . A G,T 80.82 . AC=2,2;AF=0.016,0.016;AN=128;BaseQRankSum=0.513;DP=248;Dels=0.00;FS=0.000;HaplotypeScore=138.2460;MLEAC=2,2;MLEAF=0.016,0.016;MQ=52.43;MQ0=1;MQRankSum=-2.482;QD=0.33;ReadPosRankSum=-2.922;SOR=0.954 GT:AD:DP:GQ
phytoene_synthase1 983 . T A,G 428.58 . AC=5,9;AF=0.039,0.070;AN=128;BaseQRankSum=-0.673;DP=249;Dels=0.00;FS=15.038;HaplotypeScore=139.6787;MLEAC=3,11;MLEAF=0.023,0.086;MQ=52.35;MQ0=1;MQRankSum=-6.785;QD=1.72;ReadPosRankSum=-7.156;SOR=3.639 GT:AD:DP:GQ
phytoene_synthase1 984 . G A 224.95 . AC=8;AF=0.063;AN=128;BaseQRankSum=3.123;DP=250;Dels=0.00;FS=6.380;HaplotypeScore=186.4846;MLEAC=8;MLEAF=0.063;MQ=51.99;MQ0=1;MQRankSum=-5.899;QD=0.90;ReadPosRankSum=-4.223;SOR=2.039 GT:AD:DP:GQ

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  • prateekg04prateekg04 IndiaMember

    Hi Geraldline,

    Thanks for the reply and sorry for incomplete information. I am using the UnifiedGenotyper, plz find the command below which i have used. As we have 64-fold pooled data set for a diploid organism, so we are using ploidy 128 for the analysis.

    java -jar -Xmx8g /home/prateek/Downloads/GenomeAnalysisTK.jar -T UnifiedGenotyper -R tilling.fa -I d1_S33.sorted.bam -o d1_S33.vcf -stand_call_conf 30.0 -stand_emit_conf 20.0 -glm BOTH -ploidy 128

    I am trying to attach vcf file but it is giving uploaded file type not allowed, so i have copied the complete data and paste in excel. Please find the excel file attached.

    As you can see in the excel file at positions 980, 981, 982, 984..... In altered base sometimes instead of single altered base, i am getting three or two different bases.

    Whether i am giving the right UnifiedGenotyper command or there is some mistake in that.

    Please help. Thanks in advance.

    Prateek

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