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CLI Reference

The gbcms command-line interface provides two primary commands for variant counting — one for DNA/cfDNA and one for RNA-seq — plus a normalization utility.

Commands

Command Description
dna Count alleles in DNA/cfDNA BAM files
rna Count alleles in RNA-seq BAMs with transcriptome-aware filtering
normalize Standalone variant normalization (no counting)

Quick Example

# DNA/cfDNA counting
gbcms dna \
    --variants mutations.maf \
    --bam sample1:sample1.bam \
    --bam sample2:sample2.bam \
    --fasta reference.fa \
    --output-dir results/

# RNA-seq counting
gbcms rna \
    --variants mutations.vcf \
    --bam rna_sample:star_aligned.bam \
    --fasta reference.fa \
    --output-dir results/

Getting Help

gbcms --help
gbcms dna --help
gbcms rna --help
gbcms normalize --help