vcf-sort

name	vcf-sort
description	Use when VCF files need sorting by chromosome and position, particularly before downstream analysis or indexing. Pipes VCF input through stdin.
disable-model-invocation	true
user-invocable	true

vcf-sort

Quick Start

• Command: vcf-sort [options] < input.vcf > sorted.vcf
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/vcf-sort
• Full reference: See references/help.md

When To Use This Tool

• Sort an unsorted VCF before indexing or downstream comparison.
• Apply natural chromosome ordering with -c instead of raw lexicographic order.
• Repair ordering after concatenation or ad hoc editing.
• Prefer bcftools sort in newer pipelines if you want a more actively maintained implementation.

Common Patterns

# 1) Sort a plain-text VCF from stdin
cat input.vcf | vcf-sort > sorted.vcf

# 2) Use natural chromosome ordering
zcat input.vcf.gz | vcf-sort -c > sorted.vcf

# 3) Set a custom temp directory for large sorts
zcat input.vcf.gz | vcf-sort -t /scratch > sorted.vcf

Recommended Workflow

1. Decompress or stream the input into stdin because vcf-sort is stdin-driven.
2. Use -c when chromosome-like names should follow natural version order.
3. Write the sorted output to a new file, then recompress and index it if later tools expect .vcf.gz.
4. Validate sort order before assuming region-based tools will behave correctly.

Guardrails

• This utility reads from stdin and writes to stdout; it does not take an input filename as a positional argument.
• Natural chromosome ordering with -c depends on a sort implementation that supports --version-sort.
• Header lines are preserved at the top, but malformed body records can still propagate into the output.
• Remember to bgzip and tabix the result if downstream tools require indexed compressed VCF.