New Version (1.08) is now available

[GotCloud]

A new version of gotcloud, 1.08 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

There is also a wiki page with FAQ and issues/resolutions for specific versions:

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

Summary of changes since the last release (1.07) on 7/3/2013:

Aligner

• no aligner only changes

Variant Calling

• Add the ability to copy a glf to a different directory prior to running glfExtract or glfMultiples
• Remove chromosome Y from the default CHRS. Also allow CHRS to be set on the commandline via a comma separated list specified in --chrs
• Update glfMerge to skip glf files that only have a header.
• Change default FILTER_MAX_SAMPLE_DP to 1000 (from 20)
• Some SVM updates

Aligner & Variant Calling

• Fix bug in Conf.pm that caused a failure in some versions of perl
• Add the ability to set the GOTCLOUD_ROOT so you can test with an alternate align.pl/umake.pl script and still be able to access everything else from the standard gotcloud path.
• Cleanup the perldoc for align/snpcall
• Output all configuration settings into a file when running.
• Upgrade to most current libStatGen
• Compile as optimized

Note for those at the University of Michigan: This version is already installed on the cluster and should be in your path, just type "gotcloud" to run it.

Please let me know if you have any questions.

Mary Kate Wing