Holiday Notice:
The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!

why DP value in FORMAT (sample DP, I call SNVs in one sample) is higher than DP value in INFO field?

I use haplotypecaller for SNV calling in my whole exome capture sequencing project, but I found some abnormal result in the output of haplotypecaller (version GATK 3.6).

It's abnormal to see the sample DP value is higher than DP value in INFO field, because the sample DP value is filtered coverage, but DP value in INFO field is the raw one.

chr1 887801 rs3828047 A G 1730.77 PASS ABHet=0.537;AC=1;AF=0.500;AN=2;BaseCounts=60,0,54,0;BaseQRankSum=6.959;ClippingRankSum=1.879;DB;DP=114;ExcessHet=3.0103;FS=3.780;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=1;MQRankSum=-3.411;QD=14.30;ReadPosRankSum=0.927;SOR=0.397;VariantType=SNP;set=SNP GT:AD:DP:GQ:PL 0/1:65,56:121:99:1759,0,1910

Anyone can help me with this problem?

Thanks a lot.

Tagged:
Sign In or Register to comment.