-- We use the RegenotypeVariants walker to recompute the qual field. (instead of the discussed idea of adding this functionality to CombineVariants)
-- QualByDepth will now be recomputed even if the stratified contexts are missing. This greatly improves the QD estimate for this pipeline. Doesn't work for multi-allelics since the qual can't be recomputed.
Making the usage more clear since the parameter is being used over and over to define baited
regions. Updated the headers accordingly and made it more readable.
--Previously it gave a cryptic message:
----IO error while decoding blarg.script with UTF-8
----Please try specifying another one using the -encoding option
Pool Caller scripts with last minute fixes. Also committed script that plotted 1000G FDR that I used in ASHG2012.
Added also a README.txt file in /humgen/gsa-hpprojects/dev/validationExperiments/largeScaleValidation/finalPaperData/README.txt
in case things need to get run again.
this script downsamples an exome BAM several times and makes a coverage distribution
analysis (of bases that pass filters) as well as haplotype caller calls with a NA12878
Knowledge Base assessment with comparison against multi-sample calling
with the UG.
This script was used for the "downsampling the exome" presentation
Quick fix the missing column header in the QualifyMissingIntervals
report.
Adding a QScript for the tool as well as a few minor updates to the
GATKReportGatherer.
* add a length of the overlaping interval metric as per CSER request
* standardized the distance metrics to be positive when fully overlapping and the longest off-target tail (as a negative number) when not overlapping
* add gatkdocs to the tool (finally!)
--specifying exception types in cases where none was already specified
----mostly changed to catch Exception instead of Throwable
----EmailMessage has a point where it should only be expecting a RetryException but was catching everything
--changing build.xml so that it prints scala feature warning details
--added necessary imports needed to remove feature warnings
--updating a newly deprecated enum declaration to match the new syntax
--modified ivy dependencies
--modified scala classpath in build.xml to include scala-reflect
--changed imports to point to the new scala scala.reflect.internal.util
--set the bootclasspath in QScriptManager as well as the classpath variable.
--removing Set[File] <-> Set[String] conversions
----Set is invariant now and the conversions broke
--removing unit tests for Set[File] <-> Set[String] conversions
* add a new column to do what I have been doing manually for every project, understand why we got no usable coverage in that interval
* add unit tests -- this tool is now public, we need tests.
* slightly better docs -- in an effort to produce better docs for this tool
most people don't care about excessive coverage (unless you're very
particular about your analysis). Therefore the best possible default
value for this is Integer.maxValue so it doesn't get in the way.
Itemized Changes:
* change maximumCoverage threshold to Integer.maxValue
[delivers #57353620]
Eric Banks
Ryan Poplin
kshakir
Mauricio Carneiro
Louis Bergelson
David Roazen
Guillermo del Angel
Chris Hartl
Geraldine Van der Auwera
Michael McCowan