| .. |
|
contexts
|
VariantFilteration now accepts a VCF rod in addition to an input geli. It will then annotate this VCF file with filtering information in the INFO field too. --OnlyAnnotate will not write in filtering output
|
2009-11-10 13:24:58 +00:00 |
|
datasources
|
Command-line arguments for SamReadFilters.
|
2009-11-10 23:36:17 +00:00 |
|
examples
|
Cleaned division of responsibilities between arguments to map function. Reference has been changed
|
2009-08-04 21:01:37 +00:00 |
|
executive
|
Support for initialize() and onTraversalDone() output from parallelized walkers.
|
2009-10-26 20:18:31 +00:00 |
|
filters
|
Command-line arguments for SamReadFilters.
|
2009-11-10 23:36:17 +00:00 |
|
io
|
Support for initialize() and onTraversalDone() output from parallelized walkers.
|
2009-10-26 20:18:31 +00:00 |
|
iterators
|
Take 2, updating picard with bug fix for bam files containing no reads.
|
2009-11-12 22:52:08 +00:00 |
|
refdata
|
Pileup cleanup; pooled caller v1
|
2009-11-18 17:03:48 +00:00 |
|
traversals
|
cleanup of the traversal output code
|
2009-11-12 06:18:10 +00:00 |
|
walkers
|
Pileup cleanup; pooled caller v1
|
2009-11-18 17:03:48 +00:00 |
|
CommandLineExecutable.java
|
Command-line arguments for SamReadFilters.
|
2009-11-10 23:36:17 +00:00 |
|
CommandLineGATK.java
|
adding error log reporting to the GATK, and a stream based output method for the argument collection
|
2009-10-28 19:56:05 +00:00 |
|
GATKArgumentCollection.java
|
Fix some problematic command-line argument naming and descriptions.
|
2009-11-12 02:12:26 +00:00 |
|
GenomeAnalysisEngine.java
|
Take 2, updating picard with bug fix for bam files containing no reads.
|
2009-11-12 22:52:08 +00:00 |
|
Reads.java
|
Command-line arguments for SamReadFilters.
|
2009-11-10 23:36:17 +00:00 |
|
WalkerManager.java
|
Allow users to directly specify filters from the command-line, applicable to
|
2009-11-10 18:40:16 +00:00 |
|
package.html
|
More package-level documentation.
|
2009-06-17 16:28:45 +00:00 |
6fe1c337ff