Gc getpipeupsummaries use mappingqualityreadfilter #8781
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droazen
approved these changes
Apr 18, 2024
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This looks good to me provided @davidbenjamin is also ok with it
| * <p> | ||
| * Finally for those using mappers other than bwa mem or dragen-os, {@code --minimum-mapping-quality} threshold is | ||
| * set to 50, which limits the usable reads that tool considers for generating pileups. Certain mappers are known to | ||
| * assign scores less that this threshold even for the unique mappers. If you observe all empty results in your |
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Did you mean "unique mappings" rather than "unique mappers"?
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Ah yes. Typo at midnight. I will fix it shortly.
|
This is fine with me. |
gokalpcelik
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GetPileupSummaries tool is adjusted to use the standard MappingQualityReadFilter as other walkers. Default value is set to 50 as in the original one. Old parameter set is removed and documentation is updated.