Hi there,
I used -ERC gVCF mode in Haplotyper to call variant on single sample. One of the variants listed below is present in gCVF file. I then used genotypeGVF to convert the gcvf fie to vcf file and this variant is not present in the output. Can someone help to figure out why it got filtered ?
19 7586527 . ATTT A,ATT, 49.73 . BaseQRankSum=0.764;ClippingRankSum=-1.297;DP=109;ExcessHet=3.0103;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00;MQRankSum=1.261;RAW_MQ=526843.00;ReadPosRankSum=0.871 GT:AD:DP:GQ:PL:SB 0/2:24,3,8,0:35:37:87,37,1026,0,356,372,107,479,382,487:17,7,6,5
command used to go from gVCF file to VCF file -
java -jar GenomeAnalysisTK.jar -T GenotypeGVCFs -R human_g1k_v37_decoy_and_chimerics.fasta --variant NA12878_g.vcf -o NA12878.vcf
Swati