Pipeline for calling and analyzing variants from RNA-Seq data
We provide a simpe luigi-wrapper script to set the $PYTHONPATH and --module flag for you.
./luigi-wrapper <task> <task_args>Minimally configure luigi.cfg as described in the example configuration we provide.
You only need to provide a path to a FASTA file containing a primary assembly and a GTF for gene annotations which is in turn used by STAR for read alignment.
Setup the Conda environment:
conda env create -f environment.yml
conda activate rnaseq-variant-pipeline
python setup.py install
Add your FASTQs under pipeline-output/data/<experiment_id>/<sample_id>/ and run a task described in the
following section.
| Task | Description |
|---|---|
| AlignSample | First aligment with genomic reference |
| PrepareSampleReference | Prepare a personalized genomic reference for the sample |
| AlignStep2Sample | Second alignment with sample reference |
| AddOrReplaceReadGroups | Replace read groups |
| MarkDuplicates | Mark duplicated alignments |
| SplitNCigarReads | Split N-CIGAR reads |
| CallVariants | Call variants |
| FilterVariants | Filter variants |
| FilterVariantsInExperiment | Meta-task to run all the sample of an experiment |