| 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
samtools.pl \
showALEN \
alignments.sam
samtools.pl \
varFilter \
calls.cns-pileup \
> calls.filtered.txt
samtools.pl \
pileup2fq \
calls.cns-pileup \
> consensus.fq
Recommended Workflow
- Start by choosing the subcommand, because
samtools.pl is a small helper-script collection rather than a single analysis tool.
- Confirm the input format matches the chosen subcommand, especially for the legacy
cns-pileup-based modes.
- Run the helper and redirect the text output to a new file for inspection.
- 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.
