Call status and Quality filters

In order for a variant to pass the filter, it must fall in a region with a minimum coverage of 8. In addition, the score of the variant (this is an internal value calculated by the variant caller used) must be above a specific threshold which is chosen by calculating a ROC curve (one for SNVs and another for indels) and selecting the values that give us the best trade-off between sensitivity and specificity. 

Call status can be PASS or FAIL.

  • Sentieon variant caller: variants/indels with mapping quality ≥ 100 and coverage ≥ 8 are set as PASS.
  • GATK variant caller: variants with mapping quality ≥ 85, indels with mapping quality ≥ 130, coverage ≥ 8 are set as PASS.

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