The software can be installed with conda
(best way), pip
and docker
.
The commands worfklow-hmnfusion
and workflow-fusion
must be launched with the docker image hmnfusion
.
To construct the BAM files, the command workflow-align
must be launched with the docker image hmnfusion-align
.
Install with conda
conda install -c bioconda hmnfusion
Install with pip
# Replace the <version> for the version considered
# Download from github
wget https://github.com/guillaume-gricourt/HmnFusion/releases/download/<version>/pip.zip
unzip pip.zip
# Install
pip install hmnfusion-<version>-py3-none-any.whl
# Clean up
rm pip.zip hmnfusion-<version>-py3-none-any.whl hmnfusion-<version>.tar.gz
Install with docker
Specify <version>
with digits, not using latest
# Pull the image hmnfusion
docker pull ghcr.io/guillaume-gricourt/hmnfusion:<version>
or
docker pull ggricourt/hmnfusion:<version>
# Pull the image hmnfusion-align
docker pull ggricourt/hmnfusion-align:<version>
Software is available by
hmnfusion command options
Aggregate results from Genefuse and Lumpy to produce a Json file.
hmnfusion extractfusion \ --input-genefuse-json file | --input-genefuse-html file\ --input-lumpy-vcf file \ --output-hmnfusion-json file
Calculate allelic frequency given postion or Json file produced by extractfusion
command.
A fusion is defined by two breakpoints. Only one must be in bed intervals, allelic depth is computed only on this side.
Name sample is used in vcf file.
hmnfusion quantification \ --input-hmnfusion-json file | --region chromosome:position \ --input-sample-bam file | --input-sam file \ --input-hmnfusion-bed file \ --name sample_name \ --output-hmnfusion-vcf file
Extract MMEJ information from VCF file coming from classic variant caller (GATK, Varscan, ...)
hmnfusion mmej-deletion \ --input-sample-vcf file file ... \ --input-reference-fasta file \ --output-hmnfusion-xlsx file
Extract MMEJ information from fusion breakpoints.
hmnfusion mmej-fusion \ --input-hmnfusion-json file \ --input-sample-bam file \ --input-reference-fasta file \ --name sample_name \ --output-hmnfusion-xlsx file
Run extractfusion with docker like:
docker run -it \ --rm \ hmnfusion:latest \ extractfusion \ --input-genefuse-json file | --input-genefuse-html file \ --input-lumpy-vcf file \ --output-hmnfusion-json file
Running combined extractfusion and quantification with one command-line:
docker run -it \ --rm \ hmnfusion:latest \ workflow-hmnfusion \ --input-genefuse-html file \ --input-lumpy-vcf file \ --input-sample-bam file \ --input-hmnfusion-bed file \ --name sample_name \ --output-hmnfusion-vcf file
Run with one command-line GeneFuse, Lumpy and HmnFusion:
docker run -it \ --rm \ hmnfusion:latest \ workflow-fusion \ --input-forward-fastq file \ --input-reverse-fastq file \ --input-sample-bam file \ --output-hmnfusion-vcf file \ --output-genefuse-html file \ --output-lumpy-vcf file \ --input-reference-fasta file \ --name sample_name \ --threads 4
Only the docker image hmnfusion-align could be use for this feature.
Be aware, the size of the image is near to 15Gb.
The reference files use to build BAM files could be cited with this DOI:
docker run -it \ --rm \ hmnfusion-align:latest \ workflow-align \ --input-forward-fastq file \ --input-reverse-fastq file \ --output-directory file \ --threads 4
SemVer is used for versioning.
- Guillaume Gricourt
- Dr. Ivan Sloma