with a more sensible strategy for sharding w/o BAMs at some point after
ASHG.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4549 348d0f76-0448-11de-a6fe-93d51630548a
a) Fix it up because it broke with a recent checkin to annotate vcf with unfiltered depth.
b) Printout of ref/alt alleles in output vcf was incorrect because the start/stop positions of associated GenomeLoc were incorrectly computed in case of a deletion.
c) Redid Beagle input/output walkers as not assume that ref was a single base, not to assume that variant was a vcf and generalized it to be indel-capable, so now the Beagle walkers can be used for indels as well.
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Queue GATK generated .intervals is now a List(File) again removing special case handling in the generator.
Instead of using @Scatter annotation, using ScatterFunction instance to determine if a job can be scattered.
Implemented special VcfGatherFunction which only uses the header from the first file, even if the other files differ in their headers.
Added a -deleteIntermediates to Queue to delete the outputs from intermediate commands after a successful run.
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some subset need
A C 1/1 --> C A 0/0
while another subset need
A C 1/1 --> C A 1/1
it's unclear how big these subsets are (or even if one is empty). What I do know is, doing the first one totally screws up concordance metrics for the 421-sample chip. So either something else needs to be done, or there's a bug in this walker. Until I know for sure, I've added an initialize exception to disable this thing...
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forgot to add the samples to the header. How could the VCFWriter let me get away with something so boneheaded?!
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Modified - SelectVariants: Hook up to VariantContextUtils to recalculate AC/AF/AN, which uses the accessor in VariantContext to do this. Somehow sites that were selected down to hom-ref genotypes only wound up getting positive AC.
**IMPORTANT** I kind of need input here. The header of a file used for an integration test specifies AC as being an integer. Recalculating it casts it into an integer list (which it should be, as it allows for alternate alleles). However this appears to clash with what the jexl expression is looking for? For now, the integration test itself needed to be changed -- it's unclear what to do when the header specifies AC of being one class, but recalculating it casts to another class, and I'm not sure what to do.
I'm committing my omni_qc pipeline because I'm almost certain 2 months down the road I'm going to wonder what the heck I did to generate my results.
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1: -sample can now include a file, which will be parsed for sample-name entries
2: If you request a sample to run analysis on, but it is not present in any of your RODs, VEW will exception out
3: Change added to parse Integer, String, and List<Integer> type Allele Count annotations (error otherwise)
4 [slightly problematic]: The count objects now maintain row-keys in order, as the keys were taking an inordinate amount of time in onTraversalDone (multiple calls to getRowKeys(), so many multiple sorts of the same underlying unsorted object, very bad)
There is a legacy comparison object which is unused which I will strip out soon.
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The core walker has been modified so that when variant contexts (eval and comp) are subset to command-line-specified sample(s), the chromosome count annotations (AC/AN/AF) are altered to reflect the AC/AN/AF of only those samples involved in the comparison. No more getting AC500 when you're comparing a 10-sample overlap. Interestingly enough, this didn't break any integration tests.
GenotypeConcordance now has two additional tables: Allele Count Statistics, and Allele Count Summary Statistics. These work exactly identically to the Sample Statistics and Sample Summary Statistics tables, except that the partition being used is no longer the sample, but instead the allele count of the variant sites. These tables stratify by both eval and comp ACs, e.g.
evalAC0
evalAC1
evalAC2
compAC0
compAC1
compAC2
Differences with previous integration tests were verified to only be in the Allele Count tables (by grepping them out of the diff); a new test has been added for the simple case of an AC=1 site in the eval becoming an AC=2 site in the comp.
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by the fact that the GATKSAMRecord, by design, needs to both inherit from
SAMRecord and wrap a 'member' SAMRecord, and method calls that aren't
implemented as explicit passthroughs can compromise the content of the
SAMRecord in subtle ways.
Will be automatically fixed when Picard moves to a lightweight SAMRecord
interface rather than the current heavyweight implementation. But in
the short-term, there's no obvious fix.
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that have 0 aligned bases in the genome. We'll have to fix walkers as faults
appear.
Also added JIRA GSA-406: finer-grained control of MalformedReadFilter: want
to exception out by default in these cases but pass them with a warning with
a corresponding -U flag.
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- ProduceBeagleInputWalker
+ Now takes a validation ROD and a prior to give it, will use those genotypes in place of the variant genotypes if both are present
+ Takes a bootstrap argument -- can use some given %age of the validation sites
+ Optionally takes a bootstrap output argument -- re-prints the validation VCF, filtering those sites used as part of the bootstrap
-BeagleOutputToVCFWalker
+ Now filters sites where the genotypes have been reverted to hom ref
+ Now calls in to the new VCUtils to calculate AC/AN
-Queue
+ New pipeline libraries for easy qscript creation, still a work in progress, but this is a considerable prototype
+ full calling pipeline v2 uses the above libraries
+ minor changes to some of my own scripts
+ no more need for contig interval lists, these will be parsed out of your normal interval list when it is provided
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4459 348d0f76-0448-11de-a6fe-93d51630548a
a) In Indel genotyper: we can't deal yet with extended events correctly and we are still triggering at each extended event which results in repeated records on a vcf. So, to avoid this, keep track of start position of candidate variantes we've visited and if we've visited a variant before we don't do it again.
b) Avoid infinite terms in QUAL and in genotype likelihoods which can happen if posterior AF happens to be exactly zero. For now, hard-code a minimum value of each term of the posterior AF likelihood to be -300 (ie 1e-300 in lin space). This can be solved with better and smarter log-to-lin conversions and some precision fixes in AF calculation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4455 348d0f76-0448-11de-a6fe-93d51630548a
Previous output spec contained 3 columns:
haplotypeReference,haplotypeAlternate,haplotypeStrand
where haplotypeReference was always on the + strand, and haplotypeAlternate was on the strand specified by haplotypeStrand.
The new specification contains 3 columns:
haplotypeReference,haplotypeAlternate,transcriptStrand
where haplotypeRef and haplotypeAlt are required to be on the + strand. transcriptStrand now specifies the strand of the transcript, which is needed for interpreting the haplotypes.
Bugfix #1: fix incorrect assignment of variantCodon and variantAA
(Previously variantCodon was incorrectly set to referenceCodon)
Bugfix #2: fix incorrect codingCoordStr values for - strands (bug reported by Giulio Genovese), and incorrect usage of "m." for mitochondrial transcripts (bug reported by Steve Hershman)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4444 348d0f76-0448-11de-a6fe-93d51630548a
Queue now submits new LSF jobs only after previous functions have completed successfully.
When the Queue process is shutdown (ex: via Control-C) sends a bkill command for any running jobs.
Ported commands like creating directories and scatter/gather interval list to scala functions.
Updates to LSF status tracking by porting the python to internally generated bash scripts.
Temporarily disabled job name submission to LSF. Plus side is that the full command is now available in "bjobs -w". TODO: Put back jobName passing to LSF based on an option?
Changed BaseTest to allow scala to access paths to references.
Changed the extension generator to default the analysis name to the walker "name".
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4442 348d0f76-0448-11de-a6fe-93d51630548a
Why v3, you ask? Why not? Simply because v2 was a String so old and clunky, the sun would fizzle out and grow cold before any VCF could be successfully parsed.
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Off to Yosemite in 4 hours, enjoy the week gsa folks!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4410 348d0f76-0448-11de-a6fe-93d51630548a
a) Fixed bugs in new dynamic programming-based genotyper
b) Fixed up temp hack that handles extended pileups for now.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4398 348d0f76-0448-11de-a6fe-93d51630548a
- Brought over exact AF estimation from branch (which is now dead). Exact model is default in UnifiedGenotyperV2.
- Implemented completely new genotyping algorithm given best AF estimate using dynamic programming, which in theory should be better than both greedy search and any HWE-based genotyper.
- Integrated and added new Dindel likelihood estimation model.
- Corrected annotators that would call readBasePileup: since we can be annotating extended events, best way is to interrogate context for kind of pileup and either readBasePileup or readExtendedEventPileup.
All changes above except last one are still in playground since they require more testing.
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where, when the system can't find a plugin of the correct name, the system
prefers to crap all over itself and throw an unintelligible NullPointerException
rather than displaying an intelligent error.
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the empty list. Score another victory for the integration tests.
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argument. Brought it back, and added an integrationtest to make sure it
stays around.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4390 348d0f76-0448-11de-a6fe-93d51630548a
the pileup at the next alignment start is large, we don't add as many of those
incoming reads as we should. No integration tests were affected.
Thanks, Chris!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4378 348d0f76-0448-11de-a6fe-93d51630548a
-- getToolkit().subContextFromSampleProperty(): filters a VariantContext to genotypes that come from samples that have a given property value
-- getToolkit().getSamplesWithProperty(): gets all samples with a given property
-- getToolkit().getSamplesFromVariantContext(): sample objects that are referenced by name in a VariantContext
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4361 348d0f76-0448-11de-a6fe-93d51630548a
This will allow other programs like Queue to reuse the functionality.
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pieces of core that depend on playground. Most of these have been eliminated by
(temporarily) promoting Aaron's report system to core in this checkin. I'll
follow up with other changes in separately.
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The GAE half has all the walker specific code. The new "Abstract" GAE has the rest of the logic.
More refactoring to come, with the end goal of having a tool that other java analysis programs (Queue, etc.) can use to read in genomic data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4339 348d0f76-0448-11de-a6fe-93d51630548a
Thanks to Ryan for identifying the problem.
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delangel
ebanks
hanna
fromer
chartl
kshakir
depristo
asivache
aaron
kiran
rpoplin
scalvo
bthomas
corin