bamqc

Perl scripts for generating quality control stats from BAM files

To install dependencies (requires cpanminus):

cpanm --installdeps .

To use the report generating scripts, you will also need to install the gsi-website perl module, freely available from Github.

git clone git@github.com:oicr-gsi/gsi-website.git
cd gsi-website
perl Makefile.PL
make
make install

This module also depends on samtools and Rscript being available on the path.

Installation

To install this module:

perl Makefile.PL && make && make install && make test

To run tests alone:

make test

Documentation

For man pages, see man/GSI__bamqc and man/GSI__RunReport.

To generate this documentation:

pod2text lib/GSI/bamqc.pm > man/GSI__bamqc
pod2text lib/GSI/RunReport.pm > man/GSI__RunReport

For the html pages:

pod2html --css css/style.css lib/GSI/bamqc.pm --index > docs/bamqc.html
pod2html --css css/style.css lib/GSI/RunReport.pm --index > docs/RunReport.html

Bedtools histogram files

The -H option in bamqc.pl expects a 'bedtools histogram file' for coverage. Here's how to generate this file:

samtools rmdup MY_BAM.bam - | bedtools coverage -hist -abam stdin -b targets.bed | grep all | sed 's/all/collapsed/g' >> MY_BAM.hist
bedtools coverage -hist -abam MY_BAM.bam -b targets.bed | grep all | sed 's/all/noncollapsed/g' >> MY_BAM.hist