Kristian Cibulskis 3b1ee17727 added "artifact detection mode" for PON creation ... added "str_contraction" artifact filter (improves specificity, especially in exomes) refactored out VCF constants and added descriptions added "artifact detection mode" for PON creation added "str_contraction" artifact filter (improves specificity, especially in exomes) added new dream evaulation markdown added results for SMC 4 fixed up documentation, moved location to /dsde/working/mutect/dream_smc, and checked in scala script added "artifact detection mode" for PON creation added "str_contraction" artifact filter (improves specificity, especially in exomes) fixed bug which would overwrite germline_risk filter errors updated "how to" documents and records fixed license text thinned down FP regression test from 700 sites to 100. we have better ways (DREAM, NN) to check accuracy of the method and 100 is good enough to catch regressions why oh why do the MD5-based unit tests produce different results on different machine architectures? I hate that :/ Thanks to GG, LDG and DR -- test should now produce the same results regardless of machine architecture disabled downsampling... hopefully in the final attempt to make this work cross architecture! enforced LOGLESS_CACHING... hopefully in the final final attempt to make this work cross architecture! refactored out VCF constants and added descriptions		2015-05-15 07:14:33 -04:00
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main	added "artifact detection mode" for PON creation	2015-05-15 07:14:33 -04:00
test	Rev htsjdk to version 1.132 and picard to version 1.131, and switch to using the versions in maven central	2015-05-14 15:26:23 -04:00