bio-vcf-manipulation

Operations Overview

Operation	Command	Use Case
Merge	bcftools merge	Combine samples from multiple VCFs
Concat	bcftools concat	Combine regions from multiple VCFs
Sort	bcftools sort	Sort unsorted VCF
Intersect	bcftools isec	Compare/intersect call sets
Subset	bcftools view	Extract samples or regions

bcftools merge

Goal: Combine VCF files from different samples into a single multi-sample VCF.

Approach: Use bcftools merge to join files with different sample columns at shared genomic positions.

"Merge my per-sample VCFs into one file" → Combine variant records from multiple samples into a single multi-sample VCF.

Combine multiple VCF files with different samples at the same positions.

Output missing genotypes as ./. (default)

bcftools merge sample1.vcf.gz sample2.vcf.gz -Oz -o merged.vcf.gz