PCAP-core

NGS reference implementations and helper code for mapping and mapping related stats.

This has been forked from the [ICGC-TCGA-PanCancer/PCAP-core][PCAP-core] repository as this codebase was created by cancerit and continues to be developed. This version strips out PCAWG related elements and incorporates more efficient code.

This repository contains code to run genomic alignments of paired end data and subsequent calling algorithms.

The intention is to provide reference implementations and simple to execute wrappers that are useful for the scientific community who may have little IT/bioinformatic support.

• General usage
• Docker, Singularity and Dockstore
• Dependencies/Install
• Creating a release
  • Preparation
  • Cutting the release

General usage

Available programs are described in the wiki.

Docker, Singularity and Dockstore

There are dockstore.org CWL and wrappers for this project at dockstore-cgpmap.

The docker image is held on quay.io.

The docker image is know to work correctly after import into a singularity image.

Dependencies/Install

Please be aware that this expects basic C compilation libraries and tools to be available, most are listed in INSTALL.

Please install the following before running setup.sh:

• cgpBigWig

Dependancies installed by setup.sh:

• biobambam
• bwa
• samtools

And various perl modules.

Please see the respective licence for each before use.

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.
2. Update Dockerfile to the correct version.
3. Update CHANGES.md to show major items.
4. Push commits and verify with Sanger internal CI.
5. Use the GitHub tools to draft a release.