domains / families / science / alignment-filtering

alignment-filtering

separate

Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.

When to use

• extracting specific reads
• removing low-quality alignments
• subsetting to target regions
• filtering by FLAG bits
• filtering by mapping quality
• filtering by genomic regions
• producing clean BAM files
• variant calling preparation

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