New Version of GotCloud (1.14) is now available

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GotCloud

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Aug 29, 2014, 9:20:47 AM8/29/14
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A new release of gotcloud, 1.14, is now available.  

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

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

Mary Kate Wing

General

  • Add initial beagle4 support (as a new pipeline)
  • Improve input validation
    • Add chromosome name consistency checks to all tools
  • Upgrade version of bgzf
  • Upgrade libStatGen to fix mergeBam issue.

Aligner

  • Cleanup reading of fastq index/info file
    • ignore empty lines (generates a warning)
    • compress extra tabs/trim white space
  • Validate that BWA_QUAL and BWA_THREADS settings are properly formatted

SnpCall

  • Replace glfMultiples with glfFlex
  • Validate format of BAM_INDEX file
  • Add INDEL_VCF as an alternate for INDEL_PREFIX for input indel vcfs that aren't split by chromosome.

Genotype Refinement

  • Only run beagle/thunder with more than 1 sample

Indel

  • mergeBams for a single sample as its own step (didn't work before)
  • Fix bug that it would fail if the list of files was too long
  • Add input validation
  • Validate format of BAM_INDEX file

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