pysam

combined

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines. Provides Python/HTSlib workflows for genomic files. Used when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexing, and CRAM references.

When to use

Working with sequencing alignment files (BAM/CRAM)
Analyzing genetic variants (VCF/BCF)
Extracting reference sequences or gene regions
Processing raw sequencing data (FASTQ)
Calculating coverage or read depth
Implementing bioinformatics analysis pipelines
Quality control of sequencing data
Variant calling and annotation workflows

Skill page

Conflict

The K-Dense-AI copy is a highly specific, version-pinned (pysam 0.24.1) procedural guide with bundled scripts and strict coordinate contracts. The aipoch and FreedomIntelligence copies are generic, version-agnostic overviews that rely on external reference files and lack the specific implementation details (like the `inspect_hts.py` script or specific `pileup` parameters) found in the K-Dense copy. However, the generic copies provide a broader 'When to Use' scope and a different structural approach (referencing separate markdown files for each file type) that the K-Dense copy does not fully replicate in its visible text. Combining them ensures the agent has both the high-level workflow triggers and the precise, versioned implementation details.