gbcms run

Count alleles at variant positions across one or more BAM files.

Synopsis

gbcms run [OPTIONS] --variants <FILE> --bam <NAME:PATH>... --fasta <FILE>

Required Arguments

Option	Description
--variants	VCF or MAF file with variant positions
--bam	BAM file in name:path format (can repeat)
--fasta	Reference FASTA file (with .fai index)

Output Options

Option	Default	Description
--output-dir	.	Output directory
--format	vcf	Output format (vcf or maf)
--suffix	''	Suffix for output filenames
--threads	4	Number of threads

Filtering Options

Option	Default	Description
--min-mapq	20	Minimum MAPQ
--min-baseq	0	Minimum BASEQ
--filter-duplicates	false	Filter duplicate reads
--filter-secondary	false	Filter secondary alignments
--filter-supplementary	false	Filter supplementary alignments
--filter-qc-failed	false	Filter QC failed reads
--filter-improper-pair	false	Filter improperly paired reads
--filter-indel	false	Filter reads with indels

Examples

Single BAM

gbcms run \
    --variants mutations.vcf \
    --bam sample:sample.bam \
    --fasta reference.fa \
    --output-dir results/

Multiple BAMs

gbcms run \
    --variants mutations.maf \
    --bam tumor:tumor.bam \
    --bam normal:normal.bam \
    --fasta reference.fa \
    --format maf

With Filtering

gbcms run \
    --variants mutations.vcf \
    --bam sample:sample.bam \
    --fasta reference.fa \
    --filter-duplicates \
    --min-mapq 30

Output

The command produces a VCF or MAF file with:

• Allele counts (reference and alternate depth)

• VAF (variant allele frequency)

• Strand bias (Fisher's exact test)

• Fragment counts (deduplicated)

Related

• Quick Start — Common patterns

• Nextflow Pipeline — For many samples

• Input Formats — VCF/MAF specs