gatk-3.8

History

Eric Banks c7e08965d0 The QD normalization for indels was busted and is now fixed. It is true that indels of length > 1 have higher QUALS than those of length = 1. But for the HC those QUALS are not that much higher, and it doesn't continue scaling up as the indels get larger. So we no longer normalize by indel length (which massively over-penalizes larger events and effectively drops their QD to 0). For the UG the previous normalization also wasn't perfect. Now we divide the indel length by a factor of 3 to make sure that QD is consistent over the range of indel lengths. Integration tests change because QD is different for indels. Also, got permission from Valentin to archive a failing test that no longer applies. Thanks to Kurt on the GATK forum for pointing this all out.	2014-01-13 15:23:36 -05:00
..
java	The QD normalization for indels was busted and is now fixed.	2014-01-13 15:23:36 -05:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00

Eric Banks c7e08965d0 The QD normalization for indels was busted and is now fixed.

It is true that indels of length > 1 have higher QUALS than those of length = 1.  But for the HC those
QUALS are not that much higher, and it doesn't continue scaling up as the indels get larger.  So we no
longer normalize by indel length (which massively over-penalizes larger events and effectively drops their
QD to 0).

For the UG the previous normalization also wasn't perfect.  Now we divide the indel length by a factor
of 3 to make sure that QD is consistent over the range of indel lengths.

Integration tests change because QD is different for indels.
Also, got permission from Valentin to archive a failing test that no longer applies.

Thanks to Kurt on the GATK forum for pointing this all out.

2014-01-13 15:23:36 -05:00

java

The QD normalization for indels was busted and is now fixed.

2014-01-13 15:23:36 -05:00

scala/test/org/broadinstitute/sting/queue/pipeline/examples

Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest

2013-02-27 04:45:53 -05:00