ohsu-comp-bio/compbio-galaxy-wrappers

Name: compbio-galaxy-wrappers

Owner: Oregon Health and Science University Computational Biology

Description: OHSU Galaxy wrappers.

Created: 2015-03-17 22:40:39.0

Updated: 2017-10-17 22:32:35.0

Pushed: 2018-01-10 19:31:33.0

Homepage:

Size: 1935

Language: Python

GitHub Committers

User	Most Recent Commit	# Commits
jhl667	2018-03-21 20:25:48.0	135
Jaclyn Smith	2015-11-02 21:55:37.0	31
Janice Patterson	2017-10-24 20:24:08.0	1

Other Committers

User	Email	Most Recent Commit	# Commits

README

OHSU CompBio Tools :bowtie:

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)

From Jaclyn:

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…