Process genomic sequencing data
pysamskillsetup L2★27,559
K-Dense-AI/scientific-agent-skills ↗What it does
Read, query, and analyze genomic alignment and variant files
Best for
When you need to integrate BAM, VCF, and FASTA data in a bioinformatics pipeline.
Inputs
- · BAM/SAM/CRAM alignment files
- · VCF/BCF variant files
- · FASTA/FASTQ sequences
Outputs
- · AlignedSegment / VariantRecord / sequence objects
- · coverage statistics
- · filtered reads/variants
Requires
- · Python
- · pysam
- · htslib
Preconditions
- · input files in standard genomic format
- · optional: tabix index for region queries
Failure modes
- · coordinate system confusion (0-based vs 1-based)
- · trying to fetch from non-indexed file
Trust signals
- · handles multiple file formats
- · pileup analysis for coverage
- · Pythonic interface to samtools/bcftools