sam2vcf-pl

name	sam2vcf-pl
description	Use when converting old `samtools pileup -c` output into VCF and filtering for SNP-only or indel-only calls.
disable-model-invocation	true
user-invocable	true

sam2vcf-pl

Quick Start

• Command: sam2vcf.pl [OPTIONS] < in.pileup > out.vcf
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/sam2vcf.pl
• Reference: See references/help.md

When To Use This Tool

• Convert legacy samtools pileup -c text output into VCF.
• Filter calls down to SNPs only with -s or indels only with -i.
• Keep reference alleles in the output with -R when a downstream comparison expects them.
• Rescue older pileup-based workflows that predate current bcftools calling conventions.

Common Patterns

# 1) Convert old pileup output to VCF
samtools pileup -c ref.fa alignments.bam | sam2vcf.pl > calls.vcf

# 2) Emit SNPs only
samtools pileup -c ref.fa alignments.bam | sam2vcf.pl -s > snps.vcf

# 3) Emit indels and provide the reference sequence explicitly
samtools pileup -c ref.fa alignments.bam | sam2vcf.pl -i -r ref.fa > indels.vcf

Recommended Workflow

1. Generate pileup input from an older samtools pileup -c-style workflow rather than modern mpileup defaults.
2. Decide whether you need all calls, SNPs only, or indels only before conversion.
3. Provide -r ref.fa whenever indels may appear in the input.
4. Inspect the resulting header and a few representative records before mixing this legacy VCF into newer pipelines.

Guardrails

• This script expects legacy pileup text on stdin and emits VCFv3.3, not modern VCF4 output.
• -r/--refseq is required when indels are present.
• --help works, but --version is not implemented and exits as an unknown parameter.
• Do not combine -s and -i; treat them as mutually exclusive filters.