vcf-subset

name	vcf-subset
description	Use when subsetting VCF files by samples or filtering variant types from bgzipped VCF input.
disable-model-invocation	true
user-invocable	true

vcf-subset

Quick Start

• Command: vcf-subset [OPTIONS] in.vcf.gz > out.vcf
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcf-subset
• Full reference: See references/help.md

When To Use This Tool

• Keep only a subset of samples from a compressed VCF.
• Restrict rows to certain variant classes such as SNPs or indels.
• Trim away unused alternate alleles after sample subsetting.
• Extract variants private to a subset of samples.

Common Patterns

# 1) Keep a subset of samples
vcf-subset -c samples.txt in.vcf.gz > subset.vcf

# 2) Keep only indels for one sample and drop non-variant rows
vcf-subset -c SAMPLE1 -t indels -e in.vcf.gz > sample1.indels.vcf

# 3) Keep private variants and trim unused ALTs
vcf-subset -c cases.txt -p -a in.vcf.gz > cases.private.vcf

Recommended Workflow

1. Start from a bgzipped VCF and decide whether the primary goal is sample restriction, type filtering, or privacy filtering.
2. Supply the target sample list with -c, either as a file or comma-separated list.
3. Add row-level modifiers like -t, -e, -u, -p, or -a only after thinking through their interaction.
4. Validate the resulting sample columns and variant counts before feeding the subset into association or QC workflows.

Guardrails

• Input is expected to be a bgzipped VCF.
• -f forces past missing requested samples; use it only when you understand exactly which samples are absent.
• -e excludes rows without variants in the kept subset, while -r replaces excluded sample genotypes with reference; combining them changes both row and genotype semantics.
• -a trimming alternate alleles can change ALT ordering/content, so be careful if downstream annotations depend on the original allele representation.