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:

基因組文件工具包。讀/寫 SAM/BAM/CRAM 比對、VCF/BCF 變體、FASTA/FASTQ 序列、提取區域、計算覆蓋率，用於 NGS 資料處理流程。 來源：jackspace/claudeskillz。

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