/PCAP-core

NGS reference implementations and helper code for the IGCG/TCGA Pan-Cancer Analysis Project

Primary LanguagePerlGNU General Public License v2.0GPL-2.0

ICGC-TCGA-PCAP

NGS reference implementations and helper code for the ICGC/TCGA Pan-Cancer Analysis Project

This repository contains code to run genomic alignments of paired end data and subsequent calling algorithms under a fire and forget model with automatic resume of jobs from the last successfully processed step.

The intention is to provide reference implementations but also provide simple executable wrappers that are useful for the scientific community who may have little IT support.

Some elements of this repository are specific to the ICGC/TCGA PanCancer project data submissions process.

###Dependencies/Install Some of the code included in this package has dependencies on several C packages:

And various perl modules.

Please use setup.sh to install the dependencies. Please be aware that this expects basic C compilation libraries and tools to be available.

###Programs ####bwa_aln.pl Perform paired end alignment of data using bwa backtrack algorithm - Requires BWA 0.6.2 (final stable release for this method).

####bwa_mem.pl Perform paired end alignment of data using bwa mem algorithm - Requires BWA 0.7.6a+. Please see the BWA releases for the current stable release.

###PanCancer specific ####bam_to_sra_sub.pl Generate SRA XML required for GNOS submissions.

###Utilities ####diff_bams.pl Compare two bam files ignoring differences in header information which have no effect on mapping result. @SQ number and order are expected to match.

####monitor.py Utility script which can be used to monitor CPU, memory etc for any program, e.g.

monitor.py bwa_aln.pl ...

Please be aware that all commands under this are also prefixed with:

numactl --interleave=all

##Creating a release ####Preparation

  • Commit/push all relevant changes.
  • Pull a clean version of the repo and use this for the following steps.

####Cutting the release

  1. Update lib/PCAP.pm to the correct version (adding rc/beta to end if applicable).
  2. Run ./prerelease.sh
  3. Check all tests and coverage reports are acceptable.
  4. Commit the updated docs tree and updated module/version.
  5. Push commits.
  6. Use the GitHub tools to draft a release.