pysam

SUMMARY

What it does

This skill provides procedural guidance for using pysam (version 0.24.0) to handle genomic file formats including SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, and tabix-indexed files. It covers reading, querying, filtering, writing, pileup, coverage, indexing, and CRAM reference handling. The skill includes bundled scripts for inspection and QC, and emphasizes correct coordinate conventions, header preservation, and safe writing practices. It is part of the Scientific Agent Skills library by K-Dense Inc., licensed under MIT.