gatk-3.8

History

Eric Banks 83e09b1f64 Created a new walker to do the full combination of N gVCFs from the HC single-sample ref calc pipeline. Basically, it does 3 things (as opposed to having to call into 3 separate walkers): 1. merge the records at any given position into a single one with all alleles and appropriate PLs 2. re-genotype the record using the exact AF calculation model 3. re-annotate the record using the VariantAnnotatorEngine In the course of this work it became clear that we couldn't just use the simpleMerge() method used by CombineVariants; combining HC-based gVCFs is really a complicated process. So I added a new utility method to handle this merging and pulled any related code out of CombineVariants. I tried to clean up a lot of that code, but ultimately that's out of the scope of this project. Added unit tests for correctness testing. Integration tests cannot be used yet because the HC doesn't output correct gVCFs.	2013-12-31 12:07:56 -05:00
..
java	Created a new walker to do the full combination of N gVCFs from the HC single-sample ref calc pipeline.	2013-12-31 12:07:56 -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 83e09b1f64 Created a new walker to do the full combination of N gVCFs from the HC single-sample ref calc pipeline.

Basically, it does 3 things (as opposed to having to call into 3 separate walkers):
1. merge the records at any given position into a single one with all alleles and appropriate PLs
2. re-genotype the record using the exact AF calculation model
3. re-annotate the record using the VariantAnnotatorEngine

In the course of this work it became clear that we couldn't just use the simpleMerge() method used
by CombineVariants; combining HC-based gVCFs is really a complicated process.  So I added a new
utility method to handle this merging and pulled any related code out of CombineVariants.  I tried
to clean up a lot of that code, but ultimately that's out of the scope of this project.

Added unit tests for correctness testing.
Integration tests cannot be used yet because the HC doesn't output correct gVCFs.

2013-12-31 12:07:56 -05:00

java

Created a new walker to do the full combination of N gVCFs from the HC single-sample ref calc pipeline.

2013-12-31 12:07:56 -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