exact-snp

name	exact-snp
description	Use when calling SNPs from aligned SAM/BAM reads with Subread's `exactSNP` variant caller.
disable-model-invocation	true
user-invocable	true

exact-snp

Quick Start

• Command: exactSNP -i <alignment.sam|bam> -g <reference.fa> -o <output.vcf>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/exactSNP
• Full reference: See references/help.md for complete options and examples

When To Use This Tool

• Calling SNPs from read mapping results in SAM or BAM format
• Leveraging known annotated SNPs (e.g., dbSNP) to improve calling accuracy
• Outputting discovered variants in VCF format

Common Patterns

# 1) Call SNPs from a SAM alignment
/home/vimalinx/miniforge3/envs/bio/bin/exactSNP \
  -i sample.sam \
  -g reference.fa \
  -o sample.vcf

# 2) Call SNPs from BAM with multiple threads and known SNP support
/home/vimalinx/miniforge3/envs/bio/bin/exactSNP \
  -i sample.bam \
  -b \
  -g reference.fa \
  -a known_snps.vcf.gz \
  -T 8 \
  -o sample.vcf

Recommended Workflow

1. Prepare a sorted SAM/BAM alignment file and a single FASTA reference genome
2. Optionally obtain annotated SNPs in VCF format (gzipped accepted) to supply via -a
3. Run exactSNP with required inputs (-i, -g, -o), using -b if input is BAM
4. Review the output VCF file for discovered SNPs

Guardrails

• Input alignment must be SAM or BAM; specify -b when using BAM format
• Reference genome must be a single FASTA file
• Adjust -r (minimum coverage) and -Q (q-value cutoff) to filter low-confidence calls
• The real executable name is exactSNP; exact-snp is only the skill folder name.
• Running the binary with no arguments prints the full usage banner, while -v is the real version flag (exactSNP v2.1.1).
• The output file is VCF, despite the built-in example still using a .txt suffix.