New Version of GotCloud (1.13) is now available

[GotCloud]

A new release of gotcloud, 1.13 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.  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

• Cleanup runcluster
• Upgrade to bamUtil v1.0.12a
• Upgrade to libStatGen v1.0.12
• Update README to add build instructions & wiki references

Aligner

• Increment to latest VerifyBamID

Variant Calling

• Update glfMultiples to handle when first glf is empty
• Add check for the output file before creating the .OK file
• VcfPileup - improve return codes
• Write jobfiles into a sub-directory
• Added a snpcall monitoring utility
• VcfSplit - update to only append .gz in the vcflist if there was at least one file
• Write start/stop timestamps into a logfile (generated by runcluster)

Genotype Refinement

• Update beagle2Vcf.pl to use 255 for missing PL/PL3 values
• Update vcf2Beagle and beagle2Vcf to handle biallelic indels
  • Still doesn't handle any multiallelic variants
• Added a ldrefine test.

Indel Calling

• Initial version of Indel Caller
  • Still in testing phases, if you use, please provide feedback.