variant_files

Pysam provides the VariantFile class for reading and writing VCF (Variant Call Format) and BCF (binary VCF) files. These files contain information about genetic variants, including SNPs, indels, and structural variants.

Skills
Scientific
0

What it does and how to use it

A skill that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

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Install (Claude Code)

mkdir -p .claude/skills/variant-files && curl -fsSL https://doutorai.pt/data/lib/skills__variant-files.md -o .claude/skills/variant-files/SKILL.md

Paste this command into the terminal, in your project folder, and the component installs automatically.

Content

# Working with Variant Files (VCF/BCF)

## Overview

Pysam provides the `VariantFile` class for reading and writing VCF (Variant Call Format) and BCF (binary VCF) files. These files contain information about genetic variants, including SNPs, indels, and structural variants.

## Opening Variant Files

```python
import pysam

# Reading VCF
vcf = pysam.VariantFile("example.vcf")

# Reading BCF (binary, compressed)
bcf = pysam.VariantFile("example.bcf")

# Reading compressed VCF
vcf_gz = pysam.VariantFile("example.vcf.gz")

# Writing
outvcf = pysam.VariantFile("output.vcf", "w", header=vcf.header)

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