3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Version 1.16 (Full Release on 2/25/2015)
'''General'''
'''General'''
* Update the default REF to hs37d5.fa (build 37 with decoy) and the default DBSNP_VCF to dbsnp version 142.
** You can download an updated reference at: [[GotCloud:_Genetic_Reference_and_Resource_Files#hs37d5-db142|hs37d5-db142]] (ftp://anonymous@share.sph.umich.edu/gotcloud/ref/hs37d5-db142-v1.tgz)
* Upgrade perl scripts to use <code>/usr/bin/env perl</code> instead of <code>/usr/bin/perl</code> to make it compatible with more users
* Upgrade to latest versions of libStatGen and bamUtil (versions 1.0.13)
** Fixes bug in calculating the MD5s for the fasta in polishBam
'''Aligner'''
* Update default aligner to <code>bwa mem</code>
** you can still use <code>bwa aln</code> (the previous default) by adding the following setting to your configuration file:
**:<code>MAP_TYPE = BWA</code>
* Upgrade to <code>bwa</code> version 0.7.12
* No longer call <code>verifyBamID</code> with the <code>--verbose</code> option
'''SnpCall'''
'''Genotype Refinement'''
'''Indel'''
* Cleanup pipeline.pl to reduce errors in some versions of perl
'''GenomeSTRiP'''
== Version 1.15 (Full Release on 12/16/2014) ==
== Version 1.15 (Full Release on 12/16/2014) ==
