gatk3的最后一个经典版本3.8

ebanks 686c8133ed massive change in the way the cleaner works, mostly revolving around the fact ... that we no longer trust indels from the alignments (although we do use it as a good alternate consensus possibility). Other changes include better "greedy mode" performance and allowing the user to have just the cleaned reads themselves be printed out (mostly for Matt's CleanedReadInjector). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1065 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-21 03:56:59 +00:00
R	Apprach v2. Added python analysis script, so java no longer must be used to analyses quality score data. About to refactor out lots of unneeded code	2009-06-20 16:00:23 +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	massive change in the way the cleaner works, mostly revolving around the fact	2009-06-21 03:56:59 +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	Major improvements to python analysis code -- now computes a host of statistics about quality scores from the recal_data.csv file emitted by countcovariates. Includes average Q scores, medians, modes, stdev, coefficients of variation, RSME, and % bases > q10, q20, q30. Can finally quantify and compare the improvement of quality score recalibration.	2009-06-20 19:50:37 +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	Apprach v2. Added python analysis script, so java no longer must be used to analyses quality score data. About to refactor out lots of unneeded code	2009-06-20 16:00:23 +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