vcf-concat

name	vcf-concat
description	Use when concatenating VCF files split by chromosome or when merging multiple gzipped VCFs into a single output.
disable-model-invocation	true
user-invocable	true

vcf-concat

Quick Start

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

When To Use This Tool

• Concatenate VCFs that represent adjacent genomic partitions, often by chromosome.
• Check that multiple VCFs share compatible sample columns before joining.
• Allow small overlaps with merge-sort behavior when partition boundaries are slightly messy.
• Pad missing columns with . when joining sex-chromosome or otherwise asymmetric sample tables.

Common Patterns

# 1) Concatenate chromosome-split VCFs
vcf-concat chr1.vcf.gz chr2.vcf.gz chr3.vcf.gz > cohort.vcf

# 2) Read the file list from disk
vcf-concat -f vcf_files.txt > cohort.vcf

# 3) Check column compatibility without concatenating
vcf-concat -c chr1.vcf.gz chr2.vcf.gz chr3.vcf.gz

Recommended Workflow

1. Confirm the files are truly concatenable and not meant for positional merging.
2. Use -c once before large concatenation jobs if there is any doubt about column consistency.
3. If files have small overlaps, set -s deliberately and understand that it is only a partial merge sort.
4. Recompress and index the result if later tools expect .vcf.gz.

Guardrails

• This is for concatenation of genomic partitions, not for multi-sample merging at shared loci.
• Input columns should match unless you knowingly use -p/--pad-missing.
• -s is not a general-purpose sorter; it is only for limited overlap handling.
• --version is not supported in the usual way here; use -h for interface help.