SVenX is a highly parallelized pipeline taking fastq-files (single samples or folder of several samples) generated from 10x-genomics as input and execute variant calling, annotations, filtering and genotyping resulting in a vcf-file.
Nextflow needs to be installed (https://www.nextflow.io/docs/latest/getstarted.html)
If you are working on a high performance cluster like UPPMAX:
Module load bioinfo-tools longranger vep/87 CNVnator samtools
Download
- refdata for longranger (see https://www.10xgenomics.com)
- CNVnator reference directory (https://github.com/abyzovlab/CNVnator)
- SVDB requires sciKit-learn v0.15.2 and numpy.
If you´re not working on a cluster: Install VEP + cache file (VEP ENSMBLE website), CNVnator (https://github.com/abyzovlab/CNVnator ).
Clone this repository.
git clone https://github.com/vborjesson/SVenX.git
python setup.py
Options
python SVenX_main.py -h
usage: SVenX_main.py [-h] [--sample TENX_SAMPLE] [--folder TENX_FOLDER]
[--config CONFIG] [--dryrun] [--vep] [--TIDDIT]
[--CNVnator] [--basic] [--output OUTPUT] [--nextflow NF]
SVenX takes fastq-samples generated from 10x-genomics and execute Assambly,
Variant calling, plots, stats etc. of the users choice
optional arguments:
-h, --help show this help message and exit
--sample TENX_SAMPLE Path to the 10x-genomics fastq folder
--folder TENX_FOLDER If you want to run several 10x-genomic samples at one
time, collect all in one folder and enter the path to
that folder
--config CONFIG Path to configuration file
--dryrun Add if you want to perform a dry run on longranger wgs (skip longranger wgs by adding path to already analyzed files by longranger wgs)
--vep Add if you want to run vep
--TIDDIT Add if you want to run variant calling - TIDDIT
--CNVnator Add if you want to run variant calling - CNVnator
--output OUTPUT workingDir, is set to SVenX_outs as default
--nextflow NF path to program nextflow, is set to ~/nextflow as
default
An example:
python ./SVenX_main.py --sample /home/name/project/10x_fastq_data/Sample_P3333_1001 --vep --TIDDIT --CNVnator
Or if you want to run several samples at the same time:
python ./SVenX_main.py --folder /home/name/project/10x_fastq_data --vep --TIDDIT --CNVnator
For WGS data, this pipeline takes approximately 5 days to run.