Fixed initialization of pending counts when using -startFromScratch so the count doesn't start at zero and end at -<#njobs>.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5483 348d0f76-0448-11de-a6fe-93d51630548a
ProduceBeagleInputWalker can optionally emit a beagle markers file, necessary to use the beagled reference panel for imputation. Also supports the VQSR calibration curve idea that a site can be flagged as a certain FP, based on the VQSLOD field. This allows us to have both continuous quality in the refinement of sites as well as hard filtering at some threshold so we don't end up with lots of sites with all 1/3 1/3 1/3 likelihoods for all samples (i.e., a definite FP site where we don't know anything about the samples).
Added a new VariantsToBeagleUnphased walker that writes out a marker drive hard-call unphased genotypes file suitable for imputating missing genotypes with a reference panel with beagle. Can optionally keep back a fraction of sites, marked as missing in the genotypes file, for assessment of imputation accuracy and power. The bootstrap sites can be written to a separate VCF for assessment as well.
Finally, my general Queue script for creating and evaluating reference panels from VCF files. Supports explicitly genotyping a BAM file at each panel SNP site, for assessment of imputation accuracy of a reference panel. Lots of options for exploring the impact of the VQS likelihooods, multiple VCFs for constructing the reference panel, as well as fraction of sites left out in assessing the panel's power.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5467 348d0f76-0448-11de-a6fe-93d51630548a
Also, created a standard Queue script that calculates a suite of standard indel and SNP assessment results. Will be the basis for a general evaluation Queue script with standardized data files for SNPs and Indels.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5385 348d0f76-0448-11de-a6fe-93d51630548a
- RefMetaDataTracker: grabbing variant contexts given a prefix (not sure where else this was implemented, if someone can show me I'll remove it)
- VCFUtils: grabbing VCF headers given a prefix
- MathUtils: Useful functions for calculating statistics on collections of Numbers
- VariantAnnotator: Made isUniqueHeaderLine a public static method -- maybe this should go into a different class. Not sure.
- Associations: PluginManager now used to propagate classes, implementations for Z,T,U tests, slight alteration to format to make the objects stored
in the window optionally different from those returned by whatever statistic is run across the window
Added:
- MannWhitneyU. Started to fix up WilcoxonRankSum but there are comments in there questioning the validity of some of the code, and I'm sure that
it's actually doing a U test. This implementation includes the direct calculation of p-values for small sample sizes, and a uniform approximation
for when one of the sample sets is small, and the other large. Unit tests to follow.
- BootstrapCallsMerger: takes n VCFs which have been called on the same samples; merges them together while averaging the annotations
- BootstrapCalls.q: qscript for testing the effectiveness of boostrap low-pass calling on the exome
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5372 348d0f76-0448-11de-a6fe-93d51630548a
- No more duplicate intervals
- Truncation at intervals that already exist, e.g.
exists: |--------| |-------|
new: |---------|
fixed: |-----|
note that weird instances like:
exists: |-| |-| |-|
new: |---------------------|
fixed: |----|
e.g. you're truncated to the nearest interval on whatever side. In general many behaviors could happen in this instance, this is the one currently implemented.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5323 348d0f76-0448-11de-a6fe-93d51630548a
mdcp: Some class structural changes due to the inclusion of indel calls. ApplyCut now chooses the tranche differently for each dataset.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5319 348d0f76-0448-11de-a6fe-93d51630548a
Using the name of the yaml in the log file name instead of each writing each to "queue.out" so that two yamls can run from the same directory without creating cycles in the graph.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5318 348d0f76-0448-11de-a6fe-93d51630548a
directory updates in the methods pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5305 348d0f76-0448-11de-a6fe-93d51630548a
Small fixes on the data processing pipeline
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5304 348d0f76-0448-11de-a6fe-93d51630548a
BatchMerge - additional support for indels (can't just test the alternate allele when it's an extended event, must also specify that you want to use the dindel model when you actually test the allele)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5300 348d0f76-0448-11de-a6fe-93d51630548a
TODO: Switch to bulk status checks and add status archive lookups.
Sending SIGTERM(15) instead of SIGKILL(9) to allow for graceful termination of child process.
Printing out the name of the QScripts in the compile error text.
Added a pipelineretry -PR pass through for the MFCP and MFCPTest.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5295 348d0f76-0448-11de-a6fe-93d51630548a
ExpandIntervals now checks that identical intervals are not created by (un)fortunately-spaced targets
VCFExtractIntervals no longer creates duplicate intervals in the case where a VCF has multiple entries at the same site
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5294 348d0f76-0448-11de-a6fe-93d51630548a
setting up methods development pipeline for some cosmetic changes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5277 348d0f76-0448-11de-a6fe-93d51630548a
Added a missing virtual output for the inner FCP, so that Queue can tell a run of the FCP is dot-done.
Enabled the MCFPTest for the first time, running without the tear script.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5264 348d0f76-0448-11de-a6fe-93d51630548a
Eval dbSNP's type now based on eval dbSNP instead of genotype dbSNP.
Using an external treemap instead of the JGraphT internal node set to speed up larger graph generation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5261 348d0f76-0448-11de-a6fe-93d51630548a
Pacbio pipeline: now all pacbio bams have baq annotated in so running UG is uber fast.
Methods pipeline: minor cosmetic changes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5253 348d0f76-0448-11de-a6fe-93d51630548a
. Local Indel Realignment
. Mark Duplicates
will do:
. Base Quality Score Recalibration (soon)
it's working with a single BAM for testing, but will work with a list of bam files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5250 348d0f76-0448-11de-a6fe-93d51630548a
Bug smashes for the MCFP:
Synchronized access to LSF library and modifications to the QGraph.
If values are missing from the graph with -run make sure to exit with a non-zero.
Refactored QGraph to pre-generate a unique Int for each QNode speeding up getHashCode/equals inside the graph.
Added jobPriority and removed jobLimitSeconds from QFunction.
All scatter gather is by default in a single sub directory queueScatterGather.
Moved some FCPTest into BaseTest/PipelineTest for use by MFCPTest.
Rev'ed the 1000G bams used for validation from v1 to v2 and added code to look for the bams before running other tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5247 348d0f76-0448-11de-a6fe-93d51630548a
added the ccs datasets to the pbCalling pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5233 348d0f76-0448-11de-a6fe-93d51630548a
Regular updates to the pbCalling pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5232 348d0f76-0448-11de-a6fe-93d51630548a
Added a genotypeDbsnpType and evalDbsnpType to check the extensions for .vcf or .rod.
Moved renaming of "recalibrated" bams to "cleaned" from sed to yaml generation template (see diff for more info).
Renamed fCP.q to FCP.q.
Though it's still disabled until VariantEval is updated, added changes above to the FCPTest.
Removed refseq table from the queue.sh wrapper script. Only specified in the yaml.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5213 348d0f76-0448-11de-a6fe-93d51630548a
Updated the FCP, the test, and the ADPR to handle an issue with the ADPR locating the yaml generated by the FCPTest.
Does not solve the ADPR error: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5126 348d0f76-0448-11de-a6fe-93d51630548a
Moved the BamListWriter from FCP to ListWriterFunction in the Queue core.
Added an ExampleCountLoci QScript along with an example pipeline integration test which checks MD5s.
Added a few more utility methods to PipelineTest including a currentGATK variable that points to the GATK jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5121 348d0f76-0448-11de-a6fe-93d51630548a
- Reading the refseq table from the YAML if not specified on the command line.
- Removed obsolete -bigMemQueue now that CombineVariants runs in 4g.
- Added a -mountDir /broad/software option to work around adpr automount issues.
- Merged the LSF preexec used for automount into the shell script used to execute tasks.
- Using the LSF C Library to determine when jobs are complete instead of postexec.
- Updated queue.sh to match the changes above.
- Updated the FCPTest to match the changes above.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5036 348d0f76-0448-11de-a6fe-93d51630548a
Changed the FCP.q to use an InProcessFunction work around the -runDir issue GSA-420.
Tested the FCPTest using the following dotkits and "ant clean pipelinetest -Dpipeline.run=run":
- R-2.11
- Oracle-full-client
- .cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5029 348d0f76-0448-11de-a6fe-93d51630548a
R-2.10,
Oracle-full-client,
cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
This also removes the unused titv argument
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5024 348d0f76-0448-11de-a6fe-93d51630548a
carneiro
kshakir
depristo
rpoplin
fromer
chartl
kiran
corin
ebanks
delangel