It is outputting a VCF with the 'second best guess' for the alternate allele correctly. Annotations are added at the pool level, but may get overwritten at the lane and site level. Still need to implement the merging of the the annotations at higher levels.
Calls are now made based on the likelihood AC model. Two filters are applied: minQual and minPower. Output is now a VCF file with the variant context. It's now called the gatk's PoolCaller, no longer Replication Validation framework. Lots of testing ensue....
A generalization of the parameters necessary to each class in the pool caller framework. Should make it more extensible and flexible, but I'm not yet convinced that this is the best approach. Trying it out.
DiffEngine fixed so that newInstance() would work. Pretty quickly encountered a situation where newInstance() failed. Debug output now written when this occurs in the log.
Logger now used instead of standard out, with INFO the default level.
I used this walker for my mtdna analysis where the goal was to see how the chromosomes were represented by the sequences in the bam files. It is very useful as a first look at a new dataset if you want to have an idea of where most of the reads fall. It reports the number of reads in each contig, percetages, enrichment as well as the expected number of reads for each contig and enrichment given the size of your dataset. I will document it accordingly with the new documentation tool. It's in public, and I'm happy to support it.
This is very useful if you want to output your text files or manipulate data in the usual chromosome ordering :
1
2
3
...
21
22
X
Y
GL???
...
Just use this comparator in any SortedSet class constructor and your data will be sorted like in the BAM file.
Required a significant refactoring of the GATKDoclet, which now has a unified place where the ClassDoc, class, annotation, and handler are all stored together.
Index expanded to use summary() annotation field
UserExceptions, ReadFilters, GATK engine all use the system to generate docs
Doclet expanded to handle lots of new cases
Mauricio Carneiro
Kiran V Garimella
Guillermo del Angel
Mark DePristo
Khalid Shakir