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feat: Allow read filtering based on mapping quality to junctions extract #189

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yfarjoun opened this issue Jul 3, 2024 · 0 comments · May be fixed by #194
Open

feat: Allow read filtering based on mapping quality to junctions extract #189

yfarjoun opened this issue Jul 3, 2024 · 0 comments · May be fixed by #194

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@yfarjoun
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yfarjoun commented Jul 3, 2024

Currently all reads, regardless of mapping quality are considered as valid support for junctions. However, if reads have low mapping quality, that could indicate that they are mappable elsewhere with similar alignment score. It would be an improvement to allow the user to set a mapping quality threshold, below which reads are filtered and not considered as valid support for junctions.
TimD1 added a commit to fulcrumgenomics/regtools that referenced this issue Sep 19, 2024
@TimD1
feat: added per-read flag and map quality filtering
409a492 
 - closes griffithlab#183, flag based filtering
 - closes griffithlab#189, mapping quality based filtering
 - option '-F' filters reads containing any of these flags
 - option '-f' filters reads not containing all these flags
 - option '-q' filters reads below this mapping quality
TimD1 added a commit to fulcrumgenomics/regtools that referenced this issue Sep 19, 2024
@TimD1
feat: added per-read flag and map quality filtering
548b60e 
 - closes griffithlab#183, flag based filtering
 - closes griffithlab#189, mapping quality based filtering
 - option '-F' filters reads containing any of these flags
 - option '-f' filters reads not containing all these flags
 - option '-q' filters reads below this mapping quality
@TimD1 TimD1 linked a pull request Sep 19, 2024 that will close this issue
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@TimD1 TimD1 mentioned this issue Oct 31, 2024
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feat: added per-read flag and map quality filtering fulcrumgenomics/regtools
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@yfarjoun