Read and write SAM/BAM/CRAM alignments and VCF/BCF variants using pysam.
npx skills add https://github.com/ovachiever/droid-tings --skill pysam
Please help me install this Agent Skill. Skill: pysam Source: https://github.com/ovachiever/droid-tings/tree/main/skills/pysam Command: npx skills add https://github.com/ovachiever/droid-tings --skill pysam
Pysam provides Python bindings to htslib for efficient reading, writing, and querying of SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, plus indexing and pileup analyses, enabling robust NGS pipelines.
Open a BAM file, fetch reads in a region, and fetch a FASTA sequence from the reference.
High-intent search queries and answers about installing and using this skill.
BAM files store sequencing alignments; pysam's AlignmentFile class enables random-access region queries using 0-based half-open coordinates or 1-based region strings, returning filtered reads for alignment handling and coverage analysis in NGS pipelines.
VCF files store variant calls; pysam's VariantFile provides tabix-indexed access to variants by region, enabling variant counting, annotation, and format conversion (VCF to BCF) within NGS analysis workflows.
Pysam's FastaFile enables random-access lookups of indexed reference sequences, while pileup methods compute per-base coverage and quality metrics directly from alignments, satisfying reference-aware QC and region extraction tasks.
Pysam integrates SAM/BAM/CRAM reading, VCF/BCF variant processing, and FASTA/FASTQ sequence access into unified workflows; coordinate-aware queries across formats enable alignment-to-variant linkage and comprehensive data processing.
Pysam wraps htslib, supporting CRAM compression for efficient storage and tabix indexing for rapid region retrieval across BAM, VCF, and FASTA formats, scaling to large-scale sequencing datasets.
Pysam enables SAM↔BAM↔CRAM conversion, VCF↔BCF translation, and FASTQ validation; pileup-based coverage analysis and per-base metrics support quality control and alignment assessment in production NGS pipelines.
qinyan-aiProcess SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ files via Python.
Victory-HugoQuery Ensembl genomic data via REST API for genes, sequences, variants, and coordinates.
rubenslivReads and writes bioinformatics data via a unified, HTSlib-backed Python API.
TianGzlabDetect copy number variants from exome or whole-genome sequencing data using CNVkit, GATK gCNV, or Control-FREEC.
