RELEASENOTES

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# Release Notes for HugeSeq v2.0 #
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++++ 7/14/2015 ++++

NOTE:  This is a beta release.  Several components have been modified in the package to accommodate the following changes.

## Tool "required" upgrades ##

The following upgrades are "required" for HugeSeq-2.0 to operate properly:

* GATK -> 3.2.2
* root -> 5.34.30
* pindel -> 0.2.4t
* vcftools -> 0.1.12

## Major changes since 1.2 ##

- The user can now choose to use HaplotypeCaller as well as UnifiedGenotyper for SNPs and/or Indels.
- The user can set GATK to output reference-calls. The standard format for these calls is gVCF. The file carrying the reference calls is generated in addition to the standard VCF that carries only the variants.
- The user can now choose to switch off VQSR for either or both of SNP and Indels.
- The user can now choose targeted genotyping by means of using exome target captures as input.
- The failed jobs at the VQSR stage can now be repeated without running the genotyper again by means of a new input parameter "--donegenotyping".
- The pipeline now is optimized for targeted genotyping using GATK's features for exome data processing (in --targeted mode).
- The pipeline is now capable of running VQSR on whole data set OR on chromosomes individually. This is independent of the capability to split the data into chromosomes for faster genotyping (i.e. the user can choose to do the genotyping for individual chromosomes but run VQSR on all the chromosomes collectively.)
- HugeSeq is now uses Stanovar-0.1 for annotation of variants. 

## Open issues ##
* Package has never been tested on external systems.  Unforeseen issues may arise

## Additional documents

* Refer to README file for information on Installation and Execution of the pipeline including background information about directory structure and modules used in the pipeline.