gatk-3.8/public
Mark DePristo 0c94e3d96e Adaptively compute the band pass filter from the sigma, up to a maximum size of 50 bp
-- Previously we allowed band pass filter size to be specified along with the sigma.  But now that sigma is controllable from walkers and from the command line, we instead compute the filter size given the kernel from the sigma, including all kernel points with p > 1e-5 in the kernel.  This means that if you use a smaller kernel you get a small band size and therefore faster ART
-- Update, as discussed with Ryan, the sigma and band size to 17 bp for HC (default ART wide) and max band size of 50 bp
2013-01-24 13:47:59 -05:00
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R Fix a nasty bug in reading GATK reports with a single line 2012-09-10 20:14:13 -04:00
c
chainFiles
doc
java Adaptively compute the band pass filter from the sigma, up to a maximum size of 50 bp 2013-01-24 13:47:59 -05:00
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages Remove DepthOfCoverage.java because it is no longer public 2013-01-10 11:45:38 -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 Merge branch 'master' of github.com:broadinstitute/gsa-unstable 2013-01-18 15:03:42 -05:00
testdata Reverting move of BQSR tests to public, as per DR's email 2012-07-19 10:02:05 -04:00