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pysam - Python module for reading and writing genomic datasets

Reads, writes, and manipulates SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ genomic sequences using a Pythonic interface to htslib.

Tags

Updated: 2026-09-21
bioinformaticsgenomicsngspysamsamtoolsbcftools

Capabilities

Read and write alignment filesPerform pileup coverage analysisRead and write variant filesQuery variants in genomic regions

Typical Inputs

Alignment filesVariant filesSequence files

Typical Outputs

Alignment filesVariant filesExtracted genomic sequences

What this skill does

  • Read and write alignment files
  • Perform pileup coverage analysis
  • Read and write variant files
  • Query variants in genomic regions
  • Extract reference sequences by coordinates
  • Execute samtools and bcftools commands

Inputs

  • Alignment files
  • Variant files
  • Sequence files
  • Index files
  • Genomic coordinates

Outputs

  • Alignment files
  • Variant files
  • Extracted genomic sequences
  • Coverage statistics
  • Console output

Requirements

  • Python environment
  • pysam package installation
  • Index files for random access

Source

  • Spec: SKILL.md

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