New Version of GotCloud (1.16) is now available

[GotCloud]

A new release of gotcloud, 1.16, is now available.  

Reminder, there is also a wiki page that describes the changes in each version:

http://genome.sph.umich.edu/wiki/GotCloud:_Versions

I have copied below the information on changes for this version.

There is also a wiki page with FAQ:

http://genome.sph.umich.edu/wiki/GotCloud:_FAQs

I am continually updating GotCloud based on User Suggestions.  So if you notice something, let me know and I will try to get it fixed.

The updates in this version are described below.

Please let me know if you have any questions.

The new version can be downloaded from: https://github.com/statgen/gotcloud/releases/tag/gotcloud.1.16

The latest development version is always available at: https://github.com/statgen/gotcloud

Mary Kate Wing

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: hs37d5-db142 ( ftp://anon...@share.sph.umich.edu/gotcloud/ref/hs37d5-db142-v1.tgz )
• Upgrade perl scripts to use /usr/bin/env perl instead of /usr/bin/perl 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 bwa mem
  • you can still use bwa aln (the previous default) by adding the following setting to your configuration file: *:MAP_TYPE = BWA
• Upgrade to bwa version 0.7.12
• No longer call verifyBamID with the --verbose option

SnpCall

Genotype Refinement

Indel

• Cleanup pipeline.pl to reduce errors in some versions of perl

GenomeSTRiP