Phasing and Phased Variants

DRAGEN supports output of phased variant records in the germline VCF and gVCF file. When two or more variants are phased together, the phasing information is encoded in a sample-level annotation, FORMAT/PS, that identifies which set the phased variant is in. The value in the field in an integer representing the position of the first phased variant in the set. All records in the same contig with matching PS values belong to the same set.

##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">

The following is an example of a DRAGEN single sample gVCF, where two SNPs are phased together.

chr1    1947645 .       C       T,<NON_REF>     48.44   PASS    DP=35;MQ=250.00;MQRankSum=4.983;ReadPosRankSum=3.217;FractionInformativeReads=1.000;R2_5P_bias=0.000    GT:AD:AF:DP:F1R2:F2R1:GQ:PL:SPL:ICNT:GP:PRI:SB:MB:PS    0|1:20,15,0:0.429:35:9,7,0:11,8,0:47:83,0,50,572,758,622:255,0,255:19,0:4.844e+01,8.387e-05,5.300e+01,4.500e+02,4.500e+02,4.500e+02:0.00,34.77,37.77,34.77,69.54,37.77:11,9,10,5:12,8,8,7:1947645

chr1    1947648 .       G       A,<NON_REF>     50.00   PASS    DP=36;MQ=250.00;MQRankSum=5.078;ReadPosRankSum=2.563;FractionInformativeReads=1.000;R2_5P_bias=0.000    GT:AD:AF:DP:F1R2:F2R1:GQ:PL:SPL:ICNT:GP:PRI:SB:MB:PS    1|0:16,20,0:0.556:36:8,9,0:8,11,0:48:85,0,49,734,613,698:255,0,255:16,0:5.000e+01,7.067e-05,5.204e+01,4.500e+02,4.500e+02,4.500e+02:0.00,34.77,37.77,34.77,69.54,37.77:10,6,11,9:8,8,12,8:1947645

During the genotyping step, all haplotypes and all variants are considered over an active region. For each pair of variants, if both variants occur on all of the same haplotypes, or if either is a homozygous variant, then they are phased together. If the variants only occur on different haplotypes, then they are phased opposite to each other. If any heterozygous variants are present on some of the same haplotypes but not others, phasing is aborted and no phasing information is output for the active region.