How do I convert dbSNP JSON output MAF frequencies to floats?
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Entering edit mode
19 months ago
domsooch • 0

When you pull the new dbSNP JSON format, the frequencies are given as big integers. For rs222 here are the results from the JSON format inline with their corresponding float versions. How have they encoded the numbers?? What am I missing??

   "type": "frequency",
      "value": "1000Genomes.1:9400188"  
G=0.280551/1405 (1000Genomes)   

      "type": "frequency",
      "value": "ALSPAC.1:5188058"
G=0.209393/807 (ALSPAC)  

      "type": "frequency",
      "value": "Estonian.1:3662341"
G=0.164509/737 (Estonian)  

      "type": "frequency",
      "value": "GnomAD.2:25665167"
G=0.231451/7256 (GnomAD)  

      "type": "frequency",
      "value": "NorthernSweden.1:1958226"
G=0.198333/119 (NorthernSweden)  

      "type": "frequency",
      "value": "TOPMED.2:199575429"
G=0.249251/31298 (TOPMED)  

      "type": "frequency",
      "value": "PAGE_STUDY.1:157947"
G=0.285299/22453 (PAGE_STUDY)  

      "type": "frequency",
      "value": "TWINSUK.1:5188058"
G=0.199838/741 (TWINSUK)  

      "type": "frequency",
      "value": "Vietnamese.1:1125731"
G=0.266355/57 (Vietnamese)
dbSNP JSON MAF • 365 views
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0
Entering edit mode
19 months ago
domsooch • 0

Figured it out nvrmind!!

"type": "frequency",
      "value": "TOPMED.2:199575429"
G=0.249251/31298 (TOPMED)  

 that number refers to the row_id
{
            "allele_count": 94270,
            "local_row_id": 199575429,
            "observation": {
              "deleted_sequence": "A",
              "inserted_sequence": "A",
              "position": 98531408,
              "seq_id": "NC_000002.12"
            },
            "study_name": "TOPMED",
            "study_version": 2,
            "total_count": 125568
          },

1-94270/125568=0.249251

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