Display genotype phasing

[jules-o]

With phased calls could the genotype possibly be displayed as it appears in the VCF - e.g. 0|1 rather than 0/1? Plus the phase set where available (PID field in GATK or PS in Long Ranger). That'd be a big help in identifying compound heterozygous variants where full trio data are not available, or with de novo mutations.

[hanars]

GATK does not really support phased calls so we will not be supporting this in seqr

[karynne7]

Does Seqr support GATK-phased VCFs? I'm getting errors when I try to load one, but it's ok when I remove those lines. Just want a sanity check, thanks!
Example: 1 1254443 rs1886772 G A 12553.9 PASS AC=12;AF=1;AN=12;DB;DP=312;ExcessHet=3.0103;FS=0;MLEAC=12;MLEAF=1;QD=29;SOR=0.7 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,52:52:
99:1|1:1254436_A_G:2230,156,0:1254436 1|1:0,41:41:99:1|1:1254436_A_G:1783,123,0:1254436 1|1:0,55:55:99:1|1:1254436_A_G:2406,166,0:1254436 1|1:0,66:66:99:1|1:1254436_A_G:2788,
199,0:1254436 1|1:0,28:42:84:1|1:1254436_A_G:1223,84,0:1254436 1|1:0,49:49:99:1|1:1254436_A_G:2149,147,0:1254436

[hanars]

We do not support phased VCFs at this time