pysam

SKILL.md

Pysam is a Python module for reading, manipulating, and writing genomic datasets. Read/write SAM/BAM/CRAM alignment files, VCF/BCF variant files, and FASTA/FASTQ sequences with a Pythonic interface to htslib. Query tabix-indexed files, perform pileup analysis for coverage, and execute samtools/bcftools commands.

Use the AlignmentFile class to work with aligned sequencing reads. This is appropriate for analyzing mapping results, calculating coverage, extracting reads, or quality control.

Reference: See references/alignmentfiles.md for detailed documentation on:

基因组文件工具包。读/写 SAM/BAM/CRAM 比对、VCF/BCF 变体、FASTA/FASTQ 序列、提取区域、计算覆盖率，用于 NGS 数据处理流程。 来源：jackspace/claudeskillz。

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