CLI Quick Start

Process variants with the standalone CLI.

Many samples on HPC? Use Nextflow instead.

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Basic Usage

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

Output: results/sample.vcf

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Common Options

Output Format

# VCF output (default)
gbcms run -v variants.vcf -b sample.bam -f ref.fa -o out/ --format vcf

# MAF output
gbcms run -v variants.maf -b sample.bam -f ref.fa -o out/ --format maf

Multiple Samples

# Using BAM list file
echo "sample1 /path/to/sample1.bam" > bam_list.txt
echo "sample2 /path/to/sample2.bam" >> bam_list.txt

gbcms run \
    --variants variants.vcf \
    --bam-list bam_list.txt \
    --fasta reference.fa \
    --output-dir results/

Custom Sample ID

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

Output: results/MySample.vcf

Quality Filters

gbcms run \
    --variants variants.vcf \
    --bam sample.bam \
    --fasta reference.fa \
    --output-dir results/ \
    --min-mapq 30 \
    --min-baseq 20 \
    --filter-duplicates \
    --filter-secondary

Threading

gbcms run ... --threads 8

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Complete Example

gbcms run \
    --variants variants.vcf \
    --bam TumorSample:tumor.bam \
    --fasta hg38.fa \
    --output-dir genotyped/ \
    --format vcf \
    --suffix .genotyped \
    --threads 8 \
    --min-mapq 30 \
    --min-baseq 20 \
    --filter-duplicates \
    --filter-secondary \
    --filter-supplementary

Output: genotyped/TumorSample.genotyped.vcf

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Docker

docker run --rm -v $(pwd):/data ghcr.io/msk-access/py-gbcms:2.3.0 \
    gbcms run \
    --variants /data/variants.vcf \
    --bam /data/sample.bam \
    --fasta /data/reference.fa \
    --output-dir /data/results/

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CLI Reference

gbcms run --help

Option	Default	Description
--variants	Required	VCF or MAF file
--bam	Required	BAM file(s)
--fasta	Required	Reference FASTA
--output-dir	Required	Output directory
--format	vcf	Output format (vcf/maf)
--min-mapq	20	Minimum mapping quality
--min-baseq	0	Minimum base quality
--threads	1	Number of threads

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Next Steps

• Nextflow — Process many samples in parallel

• Architecture — How it works