pe_bamtools_filtering_rules.json 431 Bytes
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{
  "filters" : [
      {
          "id" : "paired_end",
          "isPaired" : "true"
      },

      {
          "id" : "mismatch",
          "tag" : "NM:<=4"
      },

      {
          "id" : "min_size",
          "insertSize" : ">=-2000"
      },

      {
          "id" : "max_size",
          "insertSize" : "<=2000"
      }
  ],

    "rule" : " (paired_end & mismatch & min_size & max_size) | (!paired_end & mismatch) "

}