Joint Analysis for Multiple Samples

DRAGEN supports pedigree-based and population-based joint analysis for multiple samples. In pedigree-based analysis, samples from the same species are related to each other. In population-based analysis, samples of the same species are unrelated to each other.

Joint analysis requires a gVCF file for each sample. To create a gVCF file, run the germline small variant caller with the --vc-emit-ref-confidence gVCF option.

The gVCF file contains information on the variant positions and positions determined to be homozygous to the reference genome. For homozygous regions, the gVCF file includes statistics that indicate how well reads support the absence of variants or alternative alleles. Contiguous homozygous runs of bases with similar levels of confidence are grouped into blocks, referred to as hom-ref blocks. Not all entries in the gVCF are contiguous. A reference might contain gaps that are not covered by either variant line or a hom-ref block. Gaps correspond to regions that are not callable. A region is not callable if there is not at least one read mapped to the region with a MAPQ score above zero. The following example shows a joint VCF where one sample has a variant, and the other two samples are in a gVCF gap. Gaps are represented by "./.:.:".

1 605262 . G A 13.41 DRAGENHardQUAL AC=2;AF=1.000;AN=2;DP=2;FS=0.000;MQ=14.00;QD=6.70;SOR=0.693 GT:AD:AF:DP:GQ:FT:F1R2:F2R1:PL:GP ./.:.:.:.:.:LowDepth 1/1:0,2:1.000:2:4:PASS:0,0:0,2:50,6,0:1.383e+01,4.943e+00,1.951e+00 ./.:.:.:.:.:LowDepth