Changes:
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<NON_REF> likelihood in variant sites is calculated as the maximum possible likelihood for an unseen alternative allele: for reach read is calculated as the second best likelihood amongst the reported alleles.
When –ERC gVCF, stand_conf_emit and stand_conf_call are forcefully set to 0. Also dontGenotype is set to false for consistency sake.
Integration test MD5 have been changed accordingly.
Additional fix:
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Specially after adding the <NON_REF> allele, but also happened without that, QUAL values tend to go to 0 (very large integer number in log 10) due to underflow when combining GLs (GenotypingEngine.combineGLs). To fix that combineGLs has been substituted by combineGLsPrecise that uses the log-sum-exp trick.
In just a few cases this change results in genotype changes in integration tests but after double-checking using unit-test and difference between combineGLs and combineGLsPrecise in the affected integration test, the previous GT calls were either border-line cases and or due to the underflow.
Basically, it does 3 things (as opposed to having to call into 3 separate walkers):
1. merge the records at any given position into a single one with all alleles and appropriate PLs
2. re-genotype the record using the exact AF calculation model
3. re-annotate the record using the VariantAnnotatorEngine
In the course of this work it became clear that we couldn't just use the simpleMerge() method used
by CombineVariants; combining HC-based gVCFs is really a complicated process. So I added a new
utility method to handle this merging and pulled any related code out of CombineVariants. I tried
to clean up a lot of that code, but ultimately that's out of the scope of this project.
Added unit tests for correctness testing.
Integration tests cannot be used yet because the HC doesn't output correct gVCFs.
Previously, we would strip out the PLs and AD values since they were no longer accurate. However, this is not ideal because
then that information is just lost and 1) users complain on the forum and post it as a bug and 2) it gives us problems in both
the current and future (single sample) calling pipelines because we subset samples/alleles all the time and lose info.
Now the PLs and AD get correctly selected down.
While I was in there I also refactored some related code in subsetDiploidAlleles(). There were no real changes there - I just
broke it out into smaller chunks as per our best practices.
Added unit tests and updated integration tests.
Addressed reviews.
CalculatePosteriors enables the user to calculate genotype likelihood posteriors (and set genotypes accordingly) given one or more panels containing allele counts (for instance, calculating NA12878 genotypes based on 1000G EUR frequencies). The uncertainty in allele frequency is modeled by a Dirichlet distribution (parameters being the observed allele counts across each allele), and the genotype state is modeled by assuming independent draws (Hardy-Weinberg Equilibrium). This leads to the Dirichlet-Multinomial distribution.
Currently this is implemented only for ploidy=2. It should be straightforward to generalize. In addition there's a parameter for "EM" that currently does nothing but throw an exception -- another extension of this method is to run an EM over the Maximum A-Posteriori (MAP) allele count in the input sample as follows:
while not converged:
* AC = [external AC] + [sample AC]
* Prior = DirichletMultinomial[AC]
* Posteriors = [sample GL + Prior]
* sample AC = MLEAC(Posteriors)
This is more useful for large callsets with small panels than for small callsets with large panels -- the latter of these being the more common usecase.
Fully unit tested.
Reviewer (Eric) jumped in to address many of his own comments plus removed public->protected dependencies.
-- 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
* 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).
-- Previous version emitted command lines that look like:
##HaplotypeCaller="analysis_type=HaplotypeCaller input_file=[private/testdata/reduced.readNotFullySpanningDeletion.bam] ..."
the new version provides additional information on when the GATK was run and the GATK version in a nicer format:
##GATKCommandLine=<ID=HaplotypeCaller,Version=2.5-206-gbc7be2b,Date="Thu Jun 20 11:09:01 EDT 2013",Epoch=1371740941197,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[private/testdata/reduced.readNotFullySpanningDeletion.bam] read_buffer_size=null phone_home=AWS ...">
-- Additionally, the command line options are emitted sequentially in the file, so you can see a running record of how a VCF was produced, such as this example from the integration test:
##GATKCommandLine=<ID=HaplotypeCaller,Version=2.5-206-gbc7be2b,Date="Thu Jun 20 11:09:01 EDT 2013",Epoch=1371740941197,CommandLineOptions="lots of stuff">
##GATKCommandLine=<ID=SelectVariants,Version=2.5-206-gbc7be2b,Date="Thu Jun 20 11:16:23 EDT 2013",Epoch=1371741383277,CommandLineOptions="lots of stuff">
-- Removed the ProtectedEngineFeaturesIntegrationTest
-- Actual unit tests for these features!
-- Now table looks like:
Name VariantType AssessmentType Count
variant SNPS TRUE_POSITIVE 1220
variant SNPS FALSE_POSITIVE 0
variant SNPS FALSE_NEGATIVE 1
variant SNPS TRUE_NEGATIVE 150
variant SNPS CALLED_NOT_IN_DB_AT_ALL 0
variant SNPS HET_CONCORDANCE 100.00
variant SNPS HOMVAR_CONCORDANCE 99.63
variant INDELS TRUE_POSITIVE 273
variant INDELS FALSE_POSITIVE 0
variant INDELS FALSE_NEGATIVE 15
variant INDELS TRUE_NEGATIVE 79
variant INDELS CALLED_NOT_IN_DB_AT_ALL 2
variant INDELS HET_CONCORDANCE 98.67
variant INDELS HOMVAR_CONCORDANCE 89.58
-- Rewrite / refactored parts of subsetDiploidAlleles in GATKVariantContextUtils to have a BEST_MATCH assignment method that does it's best to simply match the genotype after subsetting to a set of alleles. So if the original GT was A/B and you subset to A/B it remains A/B but if you subset to A/C you get A/A. This means that het-alt B/C genotypes become A/B and A/C when subsetting to bi-allelics which is the convention in the KB. Add lots of unit tests for this functions (from 0 previously)
-- BadSites in Assessment now emits TP sites with discordant genotypes with the type GENOTYPE_DISCORDANCE and tags the expected genotype in the info field as ExpectedGenotype, such as this record:
20 10769255 . A ATGTG 165.73 . ExpectedGenotype=HOM_VAR;SupportingCallsets=ebanks,depristo,CEUTrio_best_practices;WHY=GENOTYPE_DISCORDANCE GT:AD:DP:GQ:PL 0/1:1,9:10:6:360,0,6
Indicating that the call was a HET but the expected result was HOM_VAR
-- Forbid subsetting of diploid genotypes to just a single allele.
-- Added subsetToRef as a separate specific function. Use that in the DiploidExactAFCalc in the case that you need to reduce yourself to ref only. Preserves DP in the genotype field when this is possible, so a few integration tests have changed for the UG
-- @Output isn't required for AssessNA12878
-- Previous version would could non-variant sites in NA12878 that resulted from subsetting a multi-sample VC to NA12878 as CALLED_BUT_NOT_IN_DB sites. Now they are properly skipped
-- Bugfix for subsetting samples to NA12878. Previous version wouldn't trim the alleles when subsetting down a multi-sample VCF, so we'd have false FN/FP sites at indels when the multi-sample VCF has alleles that result in the subset for NA12878 having non-trimmed alleles. Fixed and unit tested now.
-- AssessNA12878 now breaks out multi-allelics into bi-allelic components. This means that we can properly assess multi-allelic calls against the bi-allelic KB
-- Refactor AssessNA12878, moving into assess package in KB. Split out previously private classes in the walker itself into separate classes. Added real docs for all of the classes.
-- Vastly expand (from 0) unit tests for NA12878 assessments
-- Allow sites only VCs to be evaluated by Assessor
-- Move utility for creating simple VCs from a list of string alleles from GATKVariantContextUtilsUnitTest to GATKVariantContextUtils
-- Assessor bugfix for discordant records at a site. Previous version didn't handle properly the case where one had a non-matching call in the callset w.r.t. the KB, so that the KB element was eaten during the analysis. Fixed. UnitTested
-- See GSA-781 -- Handle multi-allelic variants in KB for more information
-- Bugfix for missing site counting in AssessNA12878. Previous version would count N misses for every missed value at a site. Not that this has much impact but it's worth fixing
-- UnitTests for BadSitesWriter
-- UnitTests for filtered and filtering sites in the Assessor
-- Cleanup end report generation code (simply the code). Note that instead of "indel" the new code will print out "INDELS"
-- Assessor DoC calculations now us LIBS and RBPs for the depth calculation. The previous version was broken for reduced reads. Added unit test that reads a complex reduced read example and matches the DoC of this BAM with the output of the GATK DoC tool here.
-- Added convenience constructor for LIBS using just SAMFileReader and an iterator. It's now easy to create a LIBS from a BAM at a locus. Added advanceToLocus function that moves the LIBS to a specific position. UnitTested via the assessor (which isn't ideal, but is a proper test)
-- Now supports trimming the alleles from both the reverse and forward direction.
-- Added lots of unit tests for forwrad allele trimming, as well as creating VC from forward and reverse trimming.
-- Added docs and tests for the code, to bring it up to GATK spec
The migration of org.broadinstitute.variant into the Picard repo is
complete. This commit deletes the org.broadinstitute.variant sources
from our repo and replaces it with a jar built from a checkout of the
latest Picard-public svn revision.
-Moved some of the more specialized / complex VariantContext and VCF utility
methods back to the GATK.
-Due to this re-shuffling, was able to return things like the Pair class back
to the GATK as well.
Valentin Ruano-Rubio
Eric Banks
Joel Thibault
Chris Hartl
Ryan Poplin
Michael McCowan
Mark DePristo
David Roazen