A suite of galaxy wrapped tools.
- add_af: Add the AF and DP annotations to the SAMPLE column in a VCF. NOTE: This is an old piece of code that needs to be split up in to its component parts and rewritten.
- add_hotspots: If you have forced variant calls at specific genomic loci, this will allow you to merge the hotspots VCF with a non-hotspots VCF. Mainly used to handle collisions, and to apply FILTER column annotations.
- annotate_vcf_with_bed: Given a basic BED file, annotate any instances of VCF variants overlapping regions defined in said BED file. FILTER column annotation will be applied.
- breakdancer: Detect structural variants. (https://github.com/genome/breakdancer) (http://breakdancer.sourceforge.net/)
- cnv_ptrl: Wrappers for CNV calling in amplicon sequencing data. (http://jmd.amjpathol.org/article/S1525-1578(14)00203-7/pdf)
This directory contains a pointer to UCSC's pcawg_tools repository.
To set up this repository correctly, you will need to add a submodule to your repo.
If you have not already forked and cloned this repository, the following command will allow you to pull the submodule gracefully:
git clone --recursive git@github.com:OHSUCompBio/docker_tools.git
If you have already forked and cloned this repository, but have recently updated, the pcawg_tools
directory will be empty. cd into pcawg_tools and type git submodule init.
You will see this:
Submodule 'pcwag_tools' (git@github.com:ucscCancer/pcawg_tools.git) registers for path '../pcawg_tools'
At this point, the directory will still be empty. Now perform a git submodule update.
You should see pcawg_tools being cloned into that folder, with a final note:
Submodule path '../pcawg_tools': checked out...