vcf-indel-stats

name	vcf-indel-stats
description	Use when calculating in-frame indel ratios from VCF files, optionally with exon annotations.
disable-model-invocation	true
user-invocable	true

vcf-indel-stats

Quick Start

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

When To Use This Tool

• Estimate the in-frame fraction of indels in a VCF.
• Add exon-aware context to the in-frame calculation with a simple exon interval file.
• Produce a quick textual sanity check on indel frame behavior before deeper annotation.

Common Patterns

# 1) Compute basic indel frame statistics
cat indels.vcf | vcf-indel-stats > indel_stats.txt

# 2) Use exon intervals for exon-aware stats
cat indels.vcf | vcf-indel-stats -e exons.tsv > indel_stats.txt

Recommended Workflow

1. Start from a VCF that actually contains the indels you want to summarize.
2. If coding context matters, prepare a tab-separated exon file with 1-based inclusive intervals.
3. Stream the VCF into vcf-indel-stats, optionally with -e.
4. Treat the output as a rough descriptive statistic, then escalate to richer annotation if the result matters for interpretation.

Guardrails

• Input comes from stdin.
• The exon file format is strict: chr, from, to, tab-separated, 1-based inclusive.
• This script currently reports in-frame ratio style summaries; it is not a full functional annotation engine.
• Use -v only for debugging or detailed logging, not as a substitute for validating the biological input set.