David Roazen 7d90bbab08 Add support for snpEff "GATK compatibility mode" (-o gatk) ... -Do not throw an exception when parsing snpEff output files generated by not-officially-supported versions of snpEff, PROVIDED that snpEff was run with -o gatk -Requested by the snpEff author -Relevant integration tests updated/expanded		2013-04-26 15:47:15 -04:00
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R	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -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	…
doc	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Add support for snpEff "GATK compatibility mode" (-o gatk)	2013-04-26 15:47:15 -04:00
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	Adding the 1000G_phase1.snps.high_confidence callset to the GATK resource bundle for use in the April 2013 updated best practices.	2013-04-24 11:41:32 -04:00
testdata	Updating the exampleGRP.grp test file	2013-04-13 09:07:13 -04:00