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andyrimmer / Platypus

Platypus Variant Caller
GNU General Public License v3.0
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Reference call qualities not well calibrated, and not conservative enough #12

Closed andyrimmer closed 9 years ago

andyrimmer commented 10 years ago

The QUAL values reported in REFCALL records need some work. These should always be conservative, i.e. a low score should be reported if there is any doubt about the quality of the data or if the coverage is low, or if there is any evidence for variation.

These scores currently get smeared out if the call block size is too high. One solution is to report, for the whole block, the score of the part we are least confident about.

andyrimmer commented 9 years ago

Fixed. Now use per-base min coverage for computing QUAL. Block size is configurable with --refCallBlockSize