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. FORMAT/PS 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.
Combine Phased Variants
Phased variant records that belong to the same phasing set can be combined into a single VCF record. For example, assuming reference at position chr2 115035 is A, the following two phased variants are combined.
chr2 115034 . G C GT:PS 0|1:115034
chr2 115036 . C T GT:PS 0|1:115034
The phased variants are combined as follows.
chr2 115034 . GAC CAT GT:PS 0|1:115034
You can specify the maximum distance between phased variants to be combined using the --vc-combine-phased-variants-distance command-line option. The default value is 0, which disables the option. When enabled, the option combines all phased variants in the phasing set that are within the provided distance value.
