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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)