* Refactoring implementations of readHeader(LineReader) -> readActualHeader(LineIterator), including nullary implementations where applicable.
* Galvanizing fo generic types.
* Test fixups, mostly to pass around LineIterators instead of LineReaders.
* New rev of tribble, which incorporates a fix that addresses a problem with TribbleIndexedFeatureReader reading a header twice in some instances.
* New rev of sam, to make AbstractIterator visible (was moved from picard -> sam in Tribble API refactor).
Why wasn't it there before, you ask
----------------------------------
Before I was running it separately (by hand), but now it's integrated in
the FullProcessingPipeline.
Integration was a pain because of Queue's limitation of only allowing 1
@Output file. This forced me to write the ugliest piece of code of my
life, but it's working and it's processing the YRI from scratch using
that right now. So I'm happy... somewhat.
Other changes to the pipeline
-----------------------------
* Add --filter_bases_not_stored to the IndelRealigner step -- sometimes BAM files have reads with no bases stored in the unmapped section (no idea why) but this disrupts the pipeline.
* Change adaptor marking parameter to "dual indexed" instead of "pair-ended" -- for PCR Free data.
There is now a command-line option to set the model to use in the HC.
Incorporated Ryan's current (unmerged) branch in for most of these changes.
Because small changes to the math can have drastic effects, I decided not to let users tweak
the calculations themselves. Instead they can select either NONE, CONSERVATIVE (the default),
or AGGRESSIVE.
Note that any base insertion/deletion qualities from BQSR are still used.
Also, note that the repeat unit x repeat length approach gave very poor results against the KB,
so it is not included as an option here.
* add interleaved fastq option to sam2fastq
* add optional adapter trimming path
* add "skip_revert" option to skip reverting the bams (sometimes useful -- hidden parameter)
* add a walker that reads in one bam file and outputs N bam files, one for each read group in the original bam. This is a very important step in any BAM reprocessing pipeline.
I am using this new pipeline to process the CEU and YRI PCR Free WGS
trios.
- Make -rod required
- Document that contaminationFile is currently not functional with HC
- Document liftover process more clearly
- Document VariantEval combinations of ST and VE that are incompatible
- Added a caveat about using MVLR from HC and UG.
- Added caveat about not using -mte with -nt
- Clarified masking options
- Fixed docs based on Erics comments
-- When provided, this argument causes us to only emit the selected samples into the VCF. No INFO field annotations (AC for example) or other features are modified. It's current primary use is for efficiently evaluating joint calling.
-- Add integration test for onlyEmitSamples
1) TP reviews with 0/0 genotypes were killing those sites and making them appear as assessed FPs even when correctly called!
Fixed this by changing the logic in the assessor to allow discordant genotypes through as FPs.
Also, isMonomorphic() in the MongoGenotype needs to check whether the genotype is discordant.
Added unit test for this case.
2) Minor code cleanup in the Assessor class.
The most important being the renaming of isUsableCall() to isNotUsableCall() since that's what it is returning.
-- Previous version used overlaps on the full GenomeLoc of the variant in the KB, which meant that deletions that didn't start in an interval would be included in an interval, which isn't the behavior of the tribble and so caused a mismatch when assessing variants in the knowledgebase
-- Bugfix for BAMs containing reads without real (M,I,D,N) operators. Simply needed to set validation stringency to SILENT in the read. Added a BadCigar filter to the SAMRecord stream anyway
-- Add capture all sites mode to AssessNA12878: will write all sites to the badSites VCF, regardless of whether they are bad. It's useful if you essentially want to annotate a VCF with KB information for later analysis, such as computing ROC curves
-- Add ignore filters mode to AssessNA12878: will as expected treat all sites in the input VCF calls as PASS, even if the site has a FILTER field setting
-- Add minPNonRef argument to AssessNA12878: this will consider a site not called even if the NA12878 genotype is not 0/0 if the PLs are present and the PL for 0/0 isn't greater than this value. It allows us to easily differentiate low confidence non-ref sites obtained via multi-sample calling from highly confident non-ref calls that might be real TP or FPs
-- The previous approach in VQSR was to build a GMM with the same max. number of Gaussians for the positive and negative models. However, we usually have many more positive sites than negative, so we'd prefer to use a more detailed GMM for the positive model and a less well defined model using few sites for the negative model.
-- Now the maxGaussians argument only applies to the positive model
-- This update builds a GMM for the negative model with a default 4 max gaussians (though this can be controlled via command line parameter)
-- Removes the percentBadVariants argument. The only way to control how many variants are included in the negative model is with minNumBad
-- Reduced the minNumBad argument default to 1000 from 2500
-- Update MD5s for VQSR. md5s changed significantly due to underlying changes in the default GMM model. Only sites with NEGATIVE_TRAINING_LABELs and the resulting VQSLOD are different, as expected.
-- minNumBad is now numBad
-- Plot all negative training points as well, since this significantly changes our view of the GMM PDF
-- In the case where there's some variation to assembly and evaluate but the resulting haplotypes don't result in any called variants, the reference model would exception out with "java.lang.IllegalArgumentException: calledHaplotypes must contain the refHaplotype". Now we detect this case and emit the standard no variation output.
-- [delivers #54625060]
Ami Levy-Moonshine
Eric Banks
Michael McCowan
Mauricio Carneiro
droazen
Geraldine Van der Auwera
Ryan Poplin
Mark DePristo
kshakir