| name | wgsim-eval-pl |
| description | Use when evaluating wgsim simulation results or analyzing simulated read data as part of samtools bioconda installations. |
| disable-model-invocation | true |
| user-invocable | true |
wgsim-eval-pl
Quick Start
- Command:
wgsim_eval.pl <command> [arguments]
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/wgsim_eval.pl
- Reference: See references/help.md for detailed usage
When To Use This Tool
- Evaluate alignments or variant calls produced from
wgsim-simulated data.
- Compare aligner accuracy on SAM files whose read names encode wgsim truth.
- Post-process SAM files to keep top-scoring hits before comparison.
- Compare two unique-hit alignment outputs from competing mapping workflows.
Common Patterns
wgsim_eval.pl \
alneval \
simulated.sam
wgsim_eval.pl \
alneval \
-a \
simulated.sam
wgsim_eval.pl \
vareval \
truth.wgsim.snp \
calls.pileup.flt
wgsim_eval.pl \
unique \
alignments.sam
Recommended Workflow
- Decide which task you need:
alneval, vareval, unique, or uniqcmp.
- Confirm the inputs really come from
wgsim-style simulations, because several subcommands depend on truth encoded in the read names or SNP truth files.
- Run the chosen subcommand and capture the tabular output for downstream plotting or benchmarking.
- If necessary, use
unique before alneval or uniqcmp so multi-hit alignments are normalized consistently.
Guardrails
- The first argument must be a subcommand;
--help and --version are not recognized as top-level actions.
alneval and unique expect SAM alignments whose read names were generated by wgsim; generic SAM files can produce warnings or meaningless accuracy numbers.vareval expects a wgsim.snp truth file plus a pileup-style variant call file.unique and uniqcmp are alignment post-processing/evaluation helpers, not generic SAM validation commands.
