Parse and analyze NGS alignment, variant, and sequence files with pysam.
npx skills add https://github.com/shushuzn/Rairos --skill pysam-shushuzn
Please help me install this Agent Skill. Skill: pysam Source: https://github.com/shushuzn/Rairos/tree/main/skills/pysam Command: npx skills add https://github.com/shushuzn/Rairos --skill pysam-shushuzn
Pysam streamlines NGS analysis by giving a Pythonic interface to read, query, and write genomic alignment, variant, and sequence data without stitching together many separate command-line tools.
Use the pysam skill to compute per-base coverage for chr1 from 1,000,000 to 1,000,500 from a BAM file named tumor.bam.
High-intent search queries and answers about installing and using this skill.
To calculate per-base coverage from a BAM file, use AlignmentFile to fetch reads by genomic region and run pileup-style analyses. This provides depth and per-position statistics for your specified coordinates.
To query and filter VCF variants, use VariantFile to iterate variants and access INFO/FORMAT fields and genotypes. You can apply filters and write modified VCF/BCF outputs.
The best way to extract FASTA sequences with random access is by using FastaFile with an indexed reference, enabling programmatic sequence extraction with proper coordinate handling.
Yes, you can integrate BAM, VCF, and FASTA files to validate variants with read support. This workflow also allows annotating variants with coverage and extracting sequence contexts around loci.
Yes, indexed files are required for retrieving reads from a genomic region in SAM or CRAM format. AlignmentFile relies on indexed random access to fetch reads by coordinates.
fuzzy-dynamicsAccess and manipulate SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ files in Python.
ovachieverRead and write SAM/BAM/CRAM alignments and VCF/BCF variants using pysam.
jaechang-hitsAccess and manipulate genomic data files via a Pythonic htslib interface.
galeepProvide Pythonic interfaces for SAM/BAM/CRAM and VCF/BCF genomic file operations.
