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
* 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]
-- Adding changes to CombineVariants to work with the Reference Model mode of the HaplotypeCaller.
-- Added -combineAnnotations mode to CombineVariants to merge the info field annotations by taking the median
-- Added new StrandBiasBySample genotype annotation for use in computing strand bias from single sample input vcfs
-- Bug fixes to calcGenotypeLikelihoodsOfRefVsAny, used in isActive() as well as the reference model
-- Added active region trimming capabilities to the reference model mode, not perfect yet, turn off with --dontTrimActiveRegions
-- We only realign reads in the reference model if there are non-reference haplotypes, a big time savings
-- We only realign reads in the reference model if the read is informative for a particular haplotype over another
-- GVCF blocks will now track and output the minimum PLs over the block
-- MD5 changes!
-- HC tests: from bug fixes in calcGenotypeLikelihoodsOfRefVsAny
-- GVCF tests: from HC changes above and adding in active region trimming
MauricioCarneiro
Guillermo del Angel
Chris Hartl
Eric Banks
David Roazen
Ryan Poplin
Geraldine Van der Auwera
kshakir
Michael McCowan
Louis Bergelson
chapmanb