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56 Commits (f9f8589692fece0185a7e8e059b75ee4672d1c8d)

Author SHA1 Message Date
hanna 5e8c08ee63 Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-28 20:13:01 +00:00
hanna 60fe2e06d1 Revert accidental checkin of hacked picard build. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@543 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-27 09:47:10 +00:00
jmaguire dd408a2a9a First draft of actual pooled EM caller. 
Produces sane looking output on region of 1kG pilot1:

    CALL NA12813.SRP000031.2009_02.bam CC 0.609084 0.609084
    CALL NA12003.SRP000031.2009_02.bam CC 2.114234 2.114234 CCCCC
    CALL NA06994.SRP000031.2009_02.bam CC 0.910114 0.910114 C
    CALL NA18940.SRP000031.2009_02.bam CT 2.589749 0.910114 T
    CALL NA18555.SRP000031.2009_02.bam CC 0.609084 0.609084

Next up, eval vs. Baseline pilot1 calls and pilot3 deep-coverage truth.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@525 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-24 13:42:15 +00:00
hanna 067ae09cd0 Bump picard and samtools to latest. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@207 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-27 02:26:28 +00:00
hanna 1fcf4c0cbf Update picard to work with new samtools. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@123 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-20 21:51:26 +00:00
hanna 1096bbd4d9 Moved build.xml, ivy.xml and settings to root of Sting repository. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@88 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-18 19:13:19 +00:00