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iqbal-lab-org / minos

Variant call adjudication
MIT License
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Regeno filter samples #106

Closed martinghunt closed 4 years ago

martinghunt commented 4 years ago

Adds stage at start of the regenotyping pipeline that removes samples that have "too many" non-ref variants. Cutoffs are:

  1. Too many by absolute number (default 5000)
  2. Adds up total length of REF strings. If bigger than 5% (default) of the genome length, is excluded.