sickle-in-africa/saw.structural-variants

A workflow for discovery of large structural variants in whole human genome sequences # Whole Genome Sequencing Structural Variation Workflow This github repo was originially cloned from the NBISweeden/wgs-structvar found here. ## Quick start ```bash # Install nextflow: curl -fsSL get.nextflow.io | bash mv ./nextflow ~/bin # Set work dir to no-backup, put this in your .bashrc export NXF_WORK=$SNIC_NOBACKUP/work # Pull worfklow from this repo, run manta, normalize, and variant effect predictor: nextflow run -profile milou NBISweden/wgs-structvar --project --bam --steps manta,normalize,vep # Monitor log file tail -f .nextflow.log ``` Your summary files will be in the `results` subdirectory. ## General information This is a pipeline for running the two structural variation callers fermikit and manta on UPPMAX. You can choose to run either of the two structural variation callers or both (and generate summary files). The main focus on this pipeline is to enable better comparisions with the SweGen dataset, the default parameters for the tools are the same that were used for that dataset. If you have access to the structural variants in the swegen dataset you can add that file to the pipeline and thereby have the ability to filter population specific variants. ### Profiles for running on Uppmax HPC clusters It is possible to run the pipeline in a few different ways. Either as a single-node job or letting nextflow distribute the tasks using the SLURM queing engine. There is also some slight differences in module usage depending on which HPC system is used. specify the profile to use with the `-profile` option to NextFlow: -profile milou Run on the milou cluster using the queueing system (for example, directly from the login node). -profile miloulocal Run on milou but only on the local node. Use this in a batch job on one node, reserve it for 48 hours and everything should be ok. -profile bianca The same as `milou` but on the Bianca system -profile biancalocal The same as `miloulocal` but on the Bianca system ### Masking #### Artifact …