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How to get deletions?

sridhar28sridhar28 Posts: 13Member

Dear GATK Users,

Could anybody tell me how to identify the deletions from the bam file using GATK module?? Actually i used UnifiedGenotyper i am getting list like

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT human

gi|262 48155 . G A 80.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.103;DP=10;Dels=0.00;FS=0.000;HaplotypeScore =0.0000;MLEAC=1;MLEAF=0.500;MQ=28.61;MQ0=0;MQRankSum=-1.453;QD=8.08;ReadPosRankSum=-0.336 GT:AD:DP:GQ:PL 0/1:5,5:10:99:109,0,146

Thanks Sridhar

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