Christopher Hartl 9b4f6afa21 Alterations to scripts for better performance. Grid search now expands the sens/spec tradeoff (90 was far too aggressive against hapmap chr20), and 20 max gaussians was too many, and caused errors. For consensus genotypes: remember to gunzip the beagle outputs before converting to VCF. Also, beagle can in fact create 'null' alleles in certain circumstances. I'm not sure what exactly those circumstances are, but those sites should be ignored. When it does, all alleles apear to be set to null, so this should not affect the actual phasing in the output VCF.		2012-01-20 23:07:59 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Alterations to scripts for better performance. Grid search now expands the sens/spec tradeoff (90 was far too aggressive against hapmap chr20), and 20 max gaussians was too many, and caused errors. For consensus genotypes: remember to gunzip the beagle outputs before converting to VCF. Also, beagle can in fact create 'null' alleles in certain circumstances. I'm not sure what exactly those circumstances are, but those sites should be ignored. When it does, all alleles apear to be set to null, so this should not affect the actual phasing in the output VCF.	2012-01-20 23:07:59 -05:00
test	Annotate with FS even for filtered sites	2012-01-18 22:04:51 -05:00