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Error in running variant recalibration
I am using GATK variant re calibration , it works fine on SNPs but throws an error on indel file. The error and my sample file are as follows:
ERROR MESSAGE: Your input file has a malformed header: The FORMAT field was provided but there is no genotype/sample data
##contig=<ID=17.5307,length=909> ##contig=<ID=17.5308,length=865> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Q11 Q11D1 Q11D2 Q11D4 Q11D5 1.1 1773 . TTTTGAAATATTTAGATAA T 407.08 . AC=1;AF=0.167;AN=6;BaseQRankSum=-1.076e+00;ClippingRankSum=0.00;DP=104;ExcessHet=3.0103;FS=12.041;MLEAC=1;MLEAF=0.167;MQ=56.82;MQRankSum=1.75;QD=25.44;ReadPosRankSum=1.21;SOR=1.402 GT:AD:DP:GQ:PL 0/0:55,0:55:99:0,108,1620 0:11,0:11:99:0,253 0:13,0:13:99:0,357 0:9,0:9:99:0,204 1:3,13:16:99:450,0 1.1 1792 . CTTTAAAAGAAAATACTGGACAATTTTTTGATTTGAATTGGTTTTGAAATATGAATATATTGTATAATATGAGATTAAGGTAAATTATTGAAATTCAATATATATGACATTCTTATTCTTTTTTCTGGGTTTTTTGATGATT C 407.08 . AC=1;AF=0.167;AN=6;BaseQRankSum=-6.730e-01;ClippingRankSum=1.35;DP=99;ExcessHet=3.0103;FS=12.041;MLEAC=1;MLEAF=0.167;MQ=56.82;MQRankSum=1.35;QD=25.44;ReadPosRankSum=2.56;SOR=1.402 GT:AD:DP:GQ:PL 0/0:50,0:50:55:0,55,1227 0:11,0:11:99:0,253 0:13,0:13:99:0,357 0:9,0:9:99:0,204 1:3,13:16:99:450,0