New Version of GotCloud (1.12) is now available

[GotCloud]

A new release of gotcloud, 1.12 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 and issues/resolutions for specific versions:

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

Sorry, for the delay in creating a new release.  I hope to be more prompt on releasing new versions.

I am continually updating GotCloud based on User Suggestions (and have a list that I am working through).  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.

Mary Kate Wing

Version 1.12 (Full Release on 1/17/2014)

General

• GotCloud now works when installed in a bin/ directory.
• Add tabix source and build & bgzip build
• Add some Copyright information
• Fix printing of a failed run's return code
• Upgrade to latest libStatGen & bamUtil. See links for version details.
  • Slightly newer than 1.0.10 for both - versions on 1/17/2014.
  • dedup & recab now ignore Secondary reads
  • mergeBam ignores PI header field when merging
  • Add PhoneHome - gotCloud applies a PhoneHome thinning (BAMUTIL_THINNING) defaulted to 10 (10% of the time bamUtil does PhoneHome)
• Upgrade QPLOT to ignore secondary reads
• samtools
  • Update samtools index to return an error code if it fails to build the index

Aligner

• Updgrade BWA
  • BWA_MEM is now an option
• Write timestamps to Makefile log as steps start & complete
• Remove tmp files as gotCloud goes, rather than at the end.
• Deprecate RUN_QPLOT & RUN_VERIFY_BAM_ID
  • Now the steps to run are specified in configuration.
• Mosaik
  • Upgrade to version from Oct 29, 2013
  • Add premo for pre-Mosaik processing

Variant Calling

• Update to properly handle empty VCFs
• Run make with -k option to run as much as possible after a failure.
• Update to allow steps to be dependent on BAMs (BAM_DEPEND) so they will rerun if a BAM has a newer timestamp.
• Input Validation
  • Check that BAMs exist & are not empty prior to running steps that require BAMs.
  • Check that filters min/maxDP are numbers, not fractions.
• GlfMultiples
  • update to use DP instead of GD and fix PL description in format field header
  • add region option
• samtools-hybrid
  • fail on missing BGZF EOF indicator

Genotype Refinement

• Add a default number of states to Thunder