From Genome Analysis Wiki
Jump to navigationJump to search
1,058 bytes added
, 14:48, 26 February 2015
Line 8: |
Line 8: |
| | | |
| '''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) == |