CLI Reference

The gbcms command-line interface provides a single powerful command for variant counting.

Commands

Command	Description
run	Count alleles at variant positions

Quick Example

gbcms run \
    --variants mutations.maf \
    --bam sample1:sample1.bam \
    --bam sample2:sample2.bam \
    --fasta reference.fa \
    --output-dir results/

Getting Help

gbcms --help
gbcms run --help

Related

• Quick Start — Common usage patterns
• Nextflow Pipeline — For processing many samples
• Input Formats — VCF/MAF specifications