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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 merge, normalization and QC-summary utilities.

Commands

Command Description
dna Count alleles in DNA/cfDNA BAM/CRAM files
rna Count alleles in RNA-seq BAM/CRAM files with transcriptome-aware filtering
merge Merge per-BAM-type MAFs into a single type-prefixed output
normalize Standalone variant normalization (no counting)
convert VCF ↔ MAF conversion as vcf2maf / maf2vcf write it (no counting)
summarize QC flag summary of finished outputs: text, JSON, a cohort table or MultiQC content

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
gbcms convert --help
gbcms summarize --help