ebanks cedceb33cd My only experience with getting external groups (GAP,dbSNP) to use VCF has been painful at best, so I'm not holding my breath to get indels for CG in VCF. To that extent, here's a oneoffs walker to convert from CG format to VCF for all 'del' & 'ins' types (but not 'sub' types, since they're too complex to code up in VCF and I don't care about them for now). rs ids are included. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4572 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-26 17:53:14 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	My only experience with getting external groups (GAP,dbSNP) to use VCF has been painful at best, so I'm not holding my breath to get indels for CG in VCF. To that extent, here's a oneoffs walker to convert from CG format to VCF for all 'del' & 'ins' types (but not 'sub' types, since they're too complex to code up in VCF and I don't care about them for now). rs ids are included.	2010-10-26 17:53:14 +00:00
test	Trivially phases any hom site (since it is always correct to continue the previous haplotypes by appending the same allele onto both haplotypes)	2010-10-25 16:58:41 +00:00