Mauricio Carneiro efbfdb64fe Qscript to Downsample and analyze an exome BAM ... this script downsamples an exome BAM several times and makes a coverage distribution analysis (of bases that pass filters) as well as haplotype caller calls with a NA12878 Knowledge Base assessment with comparison against multi-sample calling with the UG. This script was used for the "downsampling the exome" presentation		2013-10-10 14:37:33 -04:00
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R	Something changed with the ggtitle syntax in the latest version of ggplot2.	2013-08-14 14:40:03 -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	…
doc	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Merged bug fix from Stable into Unstable	2013-10-10 13:01:12 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -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	Qscript to Downsample and analyze an exome BAM	2013-10-10 14:37:33 -04:00
testdata	Walker to create a fastq file from an interval list	2013-06-29 11:24:16 -04:00