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Illumina / ExpansionHunter

A tool for estimating repeat sizes
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Specifying offtarget regions for loci with multiple variants #120

Closed bw2 closed 3 years ago

bw2 commented 3 years ago

Just in case this isn't a lot of work to support - for variant catalog loci with multiple variants (like HTT, FXN, etc.) it would be nice to be able to specify off-targets for one or more of the variants. For example, I tried adding them as a list of lists, but got a type error about expecting string instead of array:

{
      "LocusId": "FXN-chr9-69037286-69037304-GAA",
      "LocusStructure": "(A)*(GAA)*",
      "ReferenceRegion": [
        "9:69037261-69037286",
        "9:69037286-69037304"
      ],
      "VariantId": [
        "FXN_A",
        "FXN"
      ],
      "VariantType": [
        "Repeat",
        "RareRepeat"
      ],
      "OfftargetRegions": [
        [], [
          "chr2:220546033-220546610",
          "chr5:127247161-127247640",
          "chrX:51621350-51621856",
          "chr1:101657701-101658187",
          "chr13:102161416-102161881",
          "chr7:37848005-37848522",
          "chrY:25645531-25646013",
          "chr7:84690949-84691442",
          "chrUn_KN707747v1_decoy:1062-2074",
          "chr6:50708070-50708556",
          "chrY:24024122-24024600"
        ]
      ]
    }

Also a few places in https://github.com/Illumina/ExpansionHunter/blob/master/docs/04_VariantCatalogFiles.md say "VariantStatus" which I think is meant to say "VariantType"

bw2 commented 3 years ago

Can confirm that specifying a single list works. Thanks for the tip:

{
      "LocusId": "FXN-chr9-69037286-69037304-GAA",
      "LocusStructure": "(A)*(GAA)*",
      "ReferenceRegion": [
        "9:69037261-69037286",
        "9:69037286-69037304"
      ],
      "VariantId": [
        "FXN_A",
        "FXN"
      ],
      "VariantType": [
        "Repeat",
        "RareRepeat"
      ],
      "OfftargetRegions": [
          "chr2:220546033-220546610",
          "chr5:127247161-127247640",
          "chrX:51621350-51621856",
          "chr1:101657701-101658187",
          "chr13:102161416-102161881",
          "chr7:37848005-37848522",
          "chrY:25645531-25646013",
          "chr7:84690949-84691442",
          "chrUn_KN707747v1_decoy:1062-2074",
          "chr6:50708070-50708556",
          "chrY:24024122-24024600"
      ]

}