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Geraldine Van der Auwera 4d20c71e09 Improvements to various gatkdocs 
- Make -rod required
    - Document that contaminationFile is currently not functional with HC
    - Document liftover process more clearly
    - Document VariantEval combinations of ST and VE that are incompatible
    - Added a caveat about using MVLR from HC and UG.
    - Added caveat about not using -mte with -nt
    - Clarified masking options
    - Fixed docs based on Erics comments
 		2013-08-10 10:01:31 -07:00
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R Removed plots generation from the BaseRecalibration software 2013-06-19 14:47:56 -04:00
c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
chainFiles
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doc Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
java Improvements to various gatkdocs 2013-08-10 10:01:31 -07:00
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages ValidatingPileup was renamed to CheckPileup 2013-02-15 11:56:19 -05:00
perl Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters) 2012-06-07 16:56:32 -04:00
scala Update QScript.scala 2013-08-02 14:09:26 -04:00
testdata Walker to create a fastq file from an interval list 2013-06-29 11:24:16 -04:00