New Version (1.06) is now available

[GotCloud]

A new version of gotcloud, 1.06 is now available.

I have also created a wiki page that describes the changes in each version:

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

Summary of significant changes since the last release (1.03a) on 3/22/2013:

• Added additional optional hard-filters
• FILTER_MIN_NS - it is recommended that you use this filter and set it to your #samples/2  (It is currently set to off by default, this will likely change in a future version)
  
• Additional filters for vcfCooker can be set using: FILTER_ADDITIONAL
• It is highly recommended to add:
• FILTER_ADDITIONAL = --minQUAL 20 
• Set to 20 for deep sequencing and around 5~10, and for low coverage
  
• Added the source code for qplot
• Please cd into gotcloud/src/ and type "make"
• Moved the default configuration settings into a single file: gotcloud/bin/gotcloudDefaults.conf
• Added checks for required files prior to running.
• Add an option to merge all chromosome sites prior to running SVM (to better support targeted sequencing)
  
• Updated the interpretation of relative paths to be relative to the user's current directory
• For Aligner: Added BASE_PREFIX, FASTQ_PREFIX, and REF_PREFIX
• For Variant Caller: Added BASE_PREFIX, BAM_PREFIX, and REF_PREFIX
• These prefixes are prepended to the appropriate type of input files when relative paths are specified.
• BASE_PREFIX is prepended if the file specific prefix is not specified
• These prefixes are optional
• They can also be specified on the command-line with --base_prefix, --ref_prefix, --fastq_prefix, --bam_prefix

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