Individual skill
pysam
Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines.
scientific-skills/Data Analysis/pysam/SKILL.md
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- Last checked
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- bioinformatics Repository topic
- computational-biology Repository topic
- data-analysis Repository topic
- ai Repository topic
- biology Repository topic
- cancer-genomics Repository topic
- data-visualization Repository topic
- differential-expression Repository topic
- genomics Repository topic
- medical Repository topic
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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)
# Pysam
## When to Use
- Use this skill when you need genomic file toolkit. for reading/writing sam/bam/cram alignment files, vcf/bcf variant files, fasta/fastq sequences, extracting regions, calculating coverage, suitable for ngs data processing pipelines in a reproducible workflow.
- Use this skill when a data analytics task needs a packaged method instead of ad-hoc freeform output.
- Use this skill when the user expects a concrete deliverable, validation step, or file-based result.
- Use this skill when `the documented workflow in this package` is the most direct path to complete the request.
- Use this skill when you need the `pysam` package behavior rather than a generic answer.
## Key Features
- Scope-focused workflow aligned to: Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines.