gatk-3.8

Author	SHA1	Message	Date
kiran	e9af893bf4	Write headers that are VCF4.0 compliant git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4213 348d0f76-0448-11de-a6fe-93d51630548a	2010-09-03 23:46:27 +00:00
kiran	1c3f2be829	Change for Chris: don't depend on other Perl modules. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4053 348d0f76-0448-11de-a6fe-93d51630548a	2010-08-17 22:19:13 +00:00
kiran	23b5d71e76	A quickly hacked together replacement for AnnotateVCFwithMAF.py, which doesn't work anymore with Cancer's updated annotator. Takes an annotated MAF file and imports the annotations into the VCF file. For the MAF annotator's DNP and TNP annotations (which I think are likely to not be correct, given the lack of phasing information or even proper association to the same sample), just propagate the annotation from the previous annotated variant to which the multinucleotide polymorphism was associated. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4007 348d0f76-0448-11de-a6fe-93d51630548a	2010-08-11 00:20:08 +00:00