samtools-pl

name	samtools-pl
description	Use when working with samtools.pl, a Perl CLI utility installed by the bioconda samtools package.
disable-model-invocation	true
user-invocable	true

samtools-pl

Quick Start

• Command: samtools.pl <command> [arguments]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/samtools.pl
• Reference: See references/help.md for detailed usage information

When To Use This Tool

• Run legacy helper subcommands bundled with SAMtools.
• Compute alignment lengths from CIGAR strings with showALEN.
• Filter legacy consensus pileup variant calls with varFilter.
• Convert legacy pileup -c output into FASTQ-like consensus sequence with pileup2fq.

Common Patterns

# 1) Append alignment length derived from the CIGAR string
samtools.pl \
  showALEN \
  alignments.sam

# 2) Filter SNPs and short indels from legacy cns-pileup output
samtools.pl \
  varFilter \
  calls.cns-pileup \
  > calls.filtered.txt

# 3) Convert legacy pileup consensus output into FASTQ
samtools.pl \
  pileup2fq \
  calls.cns-pileup \
  > consensus.fq

Recommended Workflow

1. Start by choosing the subcommand, because samtools.pl is a small helper-script collection rather than a single analysis tool.
2. Confirm the input format matches the chosen subcommand, especially for the legacy cns-pileup-based modes.
3. Run the helper and redirect the text output to a new file for inspection.
4. Validate the output before using it in modern SAM/BAM/VCF workflows, since these helpers target older SAMtools pipelines.

Guardrails

• The first argument must be a subcommand such as showALEN, varFilter, or pileup2fq; -h, --help, and --version are not valid top-level actions.
• varFilter and pileup2fq operate on legacy cns-pileup output, not modern VCF or mpileup-by-default formats.
• showALEN reads SAM-like alignment text and derives an alignment length from the CIGAR string.
• This is a legacy helper script; check whether a modern native samtools or bcftools subcommand would be more appropriate before building new pipelines around it.