gatk3的最后一个经典版本3.8

kiran 9a0151b7e1 Added an option to list all available feature classes and exit. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1056 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-19 00:00:12 +00:00
R	Added R script and uncommented a line in recal_qual.py	2009-06-03 03:15:45 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	Preparation for point release of read calibrator: no artificial heap size limit, no duplicate dbsnp records.	2009-06-11 18:39:33 +00:00
java	Added an option to list all available feature classes and exit.	2009-06-19 00:00:12 +00:00
packages	Convert the somatic coverage tool to output from the packaging tool rather than from the dist target.	2009-06-18 21:29:30 +00:00
perl	checking in new folder for perl scripts AND a simple script that takes an input text file and reference dictionary (.fai) and performs stable sort of the input lines according to the contig order specified by the dictionary. Position of the contig filed to sort on in the input lines is specified as --k POS option. Input lines may specify contigs that are not in the dictionary, in this case the additional contigs will be added at the end of the sorted output, after all known contigs. The sorting order between these additional contigs is simply the order in which they first appear in the input	2009-05-27 16:34:55 +00:00
python	Script that aligns paired-end BAMs using BWA.	2009-06-18 18:14:58 +00:00
settings	Bump picard and sam to latest version.	2009-06-18 21:59:40 +00:00
shell	Adding a script for diff'ing the output of samtools and the GATK for the whole genome and each individual chromosome.	2009-06-02 21:19:39 +00:00
testdata	Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files	2009-05-14 23:20:11 +00:00
build.xml	Convert the somatic coverage tool to output from the packaging tool rather than from the dist target.	2009-06-18 21:29:30 +00:00
ivy.xml	Add bcel and cleanup.	2009-06-17 19:28:04 +00:00