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:

Boîte à outils de fichiers génomiques. Lecture/écriture des alignements SAM/BAM/CRAM, variantes VCF/BCF, séquences FASTA/FASTQ, extraction de régions, calcul de la couverture, pour les pipelines de traitement de données NGS. Source : ovachiever/droid-tings.

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