Usage¶

HmnFusion is designed to analyze some panel of genes sequenced with the aCAP-Seq library and performs with a high sensitivity and specificity 10.1016/j.jmoldx.2022.07.004

Steps¶

BAM files are analyzed by Lumpy and Genefuse
The results are aggregated by HmnFusion
Now you can calculate the fusion frequency and you can define the MMEJ sequence

These steps involved one or more commands. A workflow is available to grouped these commands into one command.

How to start with HmnFusion¶

It depends what you have:

If you have FASTQ files, you need first to create BAM files, please go to Create BAM files
If you have FASTQ, BAM files, please go to Fusion callers
If you have FASTQ, BAM files, HTML of JSON from Genefuse and VCF from Lumpy, please go to Fusion frequency or MMEJ sequences

Questions about extra files: hg19 reference, BED files ? please read the FAQ.

Create BAM files¶

It’s only available through docker

$ docker run -it \
    --rm \
    hmnfusion-align:latest \
    workflow-align \
    --input-forward-fastq <FASTQ forward, file> \
    --input-reverse-fastq <FASTQ reverse, file> \
    --output-directory <Output directory> \
    --threads 4

Fusion callers¶

It will run Genefuse, Lumpy and HmnFusion, to detect and quantify fusions.

$ hmnfusion workflow-fusion \
    # Sample
    --name <Name of sample> \
    --input-forward-fastq <Fastq file forward> \
    --input-reverse-fastq <Fastq file reverse> \
    --input-sample-bam <Bam file> \
    # Bed
    --input-genefuse-bed <Genefuse bed file> \
    --input-lumpy-bed <Lumpy bed file> \
    --input-hmnfusion-bed <HmnFusion bed file> \
    # Reference
    --input-reference-fasta <Reference fasta file (hg19)> \
    # Output
    --output-hmnfusion-vcf <Vcf file output> \
    --output-genefuse-html <Genefuse html file output> \
    --output-lumpy-vcf <Lumpy vcf file output> \
    --threads [1-6]

Fusion frequency¶

It will extract fusions from Genefuse and Lumpy to quantify them.

$ hmnfusion workflow-fusion \
    # Sample
    --input-lumpy-vcf <Lumpy Vcf file> \
    --input-genefuse-json <Genefuse, json file> OR --input-genefuse-html <Genefuse, html file> \
    --input-sample-bam <Bam file> \
    --name <Name of sample> \
    # Bed
    --input-hmnfusion-bed <HmnFusion bed file> \
    # Output
    --output-hmnfusion-vcf <Vcf file output>

MMEJ sequences¶

Define fusions of interest.

$ hmnfusion extractfusion \
    # Sample
    --input-genefuse-json <Genefuse, json file> \
    --input-genefuse-html <Genefuse, html file> \
    --input-lumpy-vcf <Lumpy vcf file> \
    # Bed
    --input-hmnfusion-bed <Bed file> \
    # Output
    --output-hmnfusion-json <Json file output>

Extract MMEJ sequences.

$ hmnfusion mmej-fusion \
    # Sample
    --input-hmnfusion-json <HmnFusion, json file> \
    --input-sample-bam <Bam file> \
    --name <Name of sample> \
    # References
    --input-reference-fasta <Reference, fasta file> \
    # Output
    --output-hmnfusion-xlsx <Excel file output> \
    --output-hmnfusion-json <Json file output>