Ryan Poplin 0cdadffe14 Committing the best of the frantic pre-CSHL experiments: Better algorithm for partioning reads amongst the alleles they support. Require the read's original alignment to actually overlap the variant. QD uses the non-informative reads when calculating D. More HC-specific annotations for potential use in a statistical filtering strategy. Increasing the minimum kmer length in the assembly graphs. Misc minor bug fixes.		2012-05-10 13:09:03 -04:00
..
R	Add warning message about ratios in variantQCreport, give ratio for MAF > 10%	2012-04-25 12:22:32 -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	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Committing the best of the frantic pre-CSHL experiments: Better algorithm for partioning reads amongst the alleles they support. Require the read's original alignment to actually overlap the variant. QD uses the non-informative reads when calculating D. More HC-specific annotations for potential use in a statistical filtering strategy. Increasing the minimum kmer length in the assembly graphs. Misc minor bug fixes.	2012-05-10 13:09:03 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Remove unnecessary and obscure usage of old R	2012-05-01 13:39:09 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Implemented getSamplesFromVCF.	2012-05-03 21:57:57 -04:00
testdata	continuing the BQSR triage...	2012-04-05 14:34:15 -04:00