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andyrimmer / Platypus

Platypus Variant Caller
GNU General Public License v3.0
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Mapping quality issue with STAR #4

Open andyrimmer opened 10 years ago

andyrimmer commented 10 years ago

STAR assigns 255 to good reads, which is supposed to be reserved for "unknown." From the manual:

The mapping quality MAPQ (column 5) is 255 for uniquely mapping reads, and int(-10*log10(1-1/Nmap)) for multi-mapping reads.

Platypus should check for this value and, optionally, allow these reads through.

iskandr commented 8 years ago

RNA aligners (including STAR) seem to typically use 255 for uniquely mapping reads. I'm not sure where the convention that MAPQ=255 is "unknown" came from for DNA aligners. Is it in the SAM spec?