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BIOSAMTOOLS (Bioinformatics)

Introduction

This module provides a Perl interface to the libbam library for indexed and unindexed SAM/BAsequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across large regions. It also provides callback functionality for calling SNPs and performing other base-by-base functions. Most operations are compatible with the BioPerl Bio::SeqFeatureI interface, allowing BAM files to be used as a backend to the GBrowse genome browser pplication (gmod.sourceforge.net).

Availability Table

Version Default Module Systems
1.38 True copper, goblin, iqaluk, monk, mosaic, orca, redfin, tembo, vdi-centos6, windeee, wobbie
1.41 True copper, goblin, iqaluk, monk, mosaic, orca, redfin, tembo, vdi-centos6, windeee, wobbie

Documentation

https://www.sharcnet.ca/help/index.php/BIOSAMTOOLS

Mailing List

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Announcements

o Oct 29, 2015: Please note according to http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.41/README it (biosamtools/1.41) only works with versions of samtools up to 0.1.19 and not with version 1.0 or higher due to major changes in the library structure. Therefore the currently installed biosamtools/1.41 module on sharcnet was built against samtools/0.1.19 also available on sharcnet. Please note there is no conflict statement in the sharcnet biosamtools/1.41 module to restrict which samtools module can be loaded, this decision is left up to the individual researcher.

Change Log

o Oct 29, 2015: Installed biosamtools/1.41 on angel, brown, copper, goblin, iqaluk, kraken, mako, monk, mosaic, orca, redfin, saw, tembo, vdi-centos6, windeee, wobbie. (hound pending)
o Aug 7, 2013: Installed 1.38 on angel,brown,goblin,hound,qaluk,kraken,monk,orca,redfin,saw.