Missing field PS from FORMAT

[olingerc]

We are starting to heavily rely on Nirvana for our annotations. Great tool together with our onsite Dragen! Today we realized, that the PS filed (phase set) found in the FORMAT column of the vcf is not found in the samples array in the json:

chr18   2555008 .       T       G       129.49  PASS    AC=2;AF=0.333;AN=6;DP=118;FS=5.441;MQ=250.00;MQRankSum=5.669;QD=1.51;ReadPosRankSum=2.742;SOR=0.576     GT:AD:AF:DP:GQ:FT:F1R2:F2R1:PL:GP:PS        0|1:17,25:0.595:42:46:PASS:9,7:8,18:85,0,45:5.0000e+01,1.2037e-04,4.7516e+01:2555002    0/0:46,0:0.000:32:84:PASS:.:.:0,84,1260:.:. 0|1:22,22:0.500:44:47:PASS:12,10:10,12:85,0,47:4.9811e+01,8.8790e-05,5.0000e+01:2555002

Any reason why this is not transferred? I am sure you did not want to transcribe all the info found in a vcf into the json but it would be great if we could include a custom choice? This would avoid having to parse two files?

"samples": [
      {
        "genotype": "0|1",
        "variantFrequencies": [
          0.5952
        ],
        "totalDepth": 42,
        "genotypeQuality": 46,
        "alleleDepths": [
          17,
          25
        ]
      },
      {
        "genotype": "0/0",
        "variantFrequencies": [
          0
        ],
        "totalDepth": 32,
        "genotypeQuality": 84,
        "alleleDepths": [
          46,
          0
        ]
      },
      {
        "genotype": "0|1",
        "variantFrequencies": [
          0.5
        ],
        "totalDepth": 44,
        "genotypeQuality": 47,
        "alleleDepths": [
          22,
          22
        ]
      }
    ],

[rajatshuvro]

Hi @olingerc , It is always a pleasure to hear from customers.

Yes, there is a way to choose which VCF info fields will be output in addition to the standard ones. You can add a command line option "--vcf-info PS" to get it. But, this feature has been recently implemented and is part of the upcoming 3.18.0 release. We hope to release that within a month or so.

Best Rajat

[olingerc]

Great to here that it is an upcoming feature! Looking forward to it. And thanks again for the application.