bio-alignment-filtering
Installation
SKILL.md
Alignment Filtering
Filter alignments by flags, quality, and regions using samtools and pysam.
Filter Flags
| Option | Description |
|---|---|
-f FLAG |
Include reads with ALL bits set |
-F FLAG |
Exclude reads with ANY bits set |
-G FLAG |
Exclude reads with ALL bits set |
-q MAPQ |
Minimum mapping quality |
-L BED |
Include reads overlapping regions |