CLI Quick Start

This guide shows you how to get started with py-gbcms using the standalone CLI for processing one or a few samples.

Processing many samples? Use the Nextflow Workflow instead for automatic parallelization on HPC clusters.

Prerequisites

• Python >= 3.10

• Rust toolchain (for installation from source)

• BAM files with index (.bai)

• Reference FASTA with index (.fai)

• Variants file (VCF or MAF)

Install via pip install py-gbcms or see the project README for detailed setup instructions.

Basic Usage

Single Sample

Count variants for one sample:

gbcms run \
    --variants variants.vcf \
    --bam sample1.bam \
    --fasta reference.fa \
    --output-dir results/

Output: results/sample1.vcf

Multiple Samples

Process multiple samples sequentially:

# Sample 1
gbcms run --variants variants.vcf --bam sample1.bam --fasta ref.fa --output-dir results/

# Sample 2
gbcms run --variants variants.vcf --bam sample2.bam --fasta ref.fa --output-dir results/

# Sample 3
gbcms run --variants variants.vcf --bam sample3.bam --fasta ref.fa --output-dir results/

Or use a BAM list file:

# Create bam_list.txt with:
# sample1 /path/to/sample1.bam
# sample2 /path/to/sample2.bam

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

Note: The CLI processes samples sequentially. For parallel processing of many samples, use the Nextflow Workflow.

Common Options

Output Format

VCF (default):

gbcms run --variants variants.vcf --bam sample.bam --fasta ref.fa --output-dir results/ --format vcf

MAF:

gbcms run --variants variants.maf --bam sample.bam --fasta ref.fa --output-dir results/ --format maf

Custom Sample IDs

Override the sample name:

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

Output: results/MySampleID.vcf

Output Suffix

Add suffix to output filenames:

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

Output: results/sample.genotyped.vcf

Threading

Use multiple threads for processing:

gbcms run \
    --variants variants.vcf \
    --bam sample.bam \
    --fasta reference.fa \
    --output-dir results/ \
    --threads 4

Quality Filters

Minimum mapping quality:

gbcms run --variants variants.vcf --bam sample.bam --fasta ref.fa --output-dir results/ --min-mapq 30

Minimum base quality:

gbcms run --variants variants.vcf --bam sample.bam --fasta ref.fa --output-dir results/ --min-baseq 20

Filter duplicates (default: enabled):

gbcms run --variants variants.vcf --bam sample.bam --fasta ref.fa --output-dir results/ --filter-duplicates

Filter secondary alignments:

gbcms run --variants variants.vcf --bam sample.bam --fasta ref.fa --output-dir results/ --filter-secondary

Complete Example

Process a sample with strict filtering:

gbcms run \
    --variants variants.vcf \
    --bam TumorSample:tumor.bam \
    --fasta hg19.fa \
    --output-dir genotyped_results/ \
    --format vcf \
    --suffix .genotyped \
    --threads 8 \
    --min-mapq 30 \
    --min-baseq 20 \
    --filter-duplicates \
    --filter-secondary \
    --filter-supplementary

Output: genotyped_results/TumorSample.genotyped.vcf

Using Docker

Run via Docker container:

docker run --rm -v $(pwd):/data ghcr.io/msk-access/py-gbcms:2.0.0 \
    gbcms run \
    --variants /data/variants.vcf \
    --bam /data/sample.bam \
    --fasta /data/reference.fa \
    --output-dir /data/results/

Next Steps

• Many samples on HPC: See Nextflow Workflow

• Usage patterns: See Usage Overview