Fixed escaping expressions that have more than one space between arguments.
Updated example to match the wiki.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5516 348d0f76-0448-11de-a6fe-93d51630548a
VCF gathering passes on the no_header and sites_only flags to CombineVariants.
Fixed deletion of gathered log files. Although they are intermediate and do not need to be re-run if not present, they should not be deleted.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5508 348d0f76-0448-11de-a6fe-93d51630548a
JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar.
JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar.
Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath.
Walkers from the GATK package are now also embedded into the Queue package.
Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP.
Removed the GATK jar argument from the example QScripts.
Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts:
1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers.
2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3
Removed other unused code.
Re-fixed dry run function ordering.
Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a
schedule file infrastructure has been restored, and is now a single file.
Only the exact bins required for the traversal are stored in the schedule.
Very close to being able to merge schedule entries.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5497 348d0f76-0448-11de-a6fe-93d51630548a
- now it differentiates between confident REF calls and not confident calls.
- you can now use a BAM file as the truth set.
- output is much clearer now
dataProcessingPipeline version 2, ready to be used.
- All the processing is now done at the sample level
- Reads the input bam file headers to combine all lanes of the same sample.
- Cleaning is now scattered/gathered. Inteligently breaks down in as many intervals as possible, given the dataset.
- Outputs one processed bam file per sample (and a .list file with all processed files listed)
- Much faster, low pass (read Papuans) can run in the hour queue.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5493 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
a) Scrapped the way in which we constructed candidate haplotypes because it wasnt fully correct and yielded corner conditions with incorrect genotyping and likelihood computation. Ideally, a haplotype should "cover" the read and the most likely alignments should be such that the ends of the read are inside the ends of the haplotype. This wasn't happening, and if you have a "dangling read off a haplotype" the probabilistic alignment model may prefer to shift a read instead of scoring it correctly - this is especially bad with tandem repeat insertions.
So now, we build haplotypes based on the reference context and adaptively change them based on read alignment positions, plus some padding and uncertainty in the alignment.
b) Changed the way soft clipped based are dealt with. Instead of either ignoring them or using them, we only use them if the read start or end position (after soft clipping) are within eventDistance of the current location. This is done because it's very common that BWA's strictly local SW implementation will soft clip every single read at an insertion position because it couldn't place that end of the read without too many mismatches, but the read is legit and the bases are good quality. If we don't take these bases into consideration, reads which are informative of an insertion event are essentially discarded because the informative part is clipped away.
c) Several cleanups and fixes to the context-dependent gap penalty model based on length of HRun.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5464 348d0f76-0448-11de-a6fe-93d51630548a
indexes'. Not yet elegant, but proves that it circumvents the performance
issues associated with the meta-index.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5454 348d0f76-0448-11de-a6fe-93d51630548a
IndelUtils: added a isInsideExtendedIndel() method to filter the above mentioned.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5449 348d0f76-0448-11de-a6fe-93d51630548a
VariantEval: now sports the new MendelianViolation utility class.
MendelianViolationClassifier: I noticed I had broken chartl's walker by changing VariantEval, so I took the liberty to modify it to use the new library too, though I kept modifications to a minimum, could have gone into full integration if this is a useful tool, but since it's in oneoffs, I decided not to go all out.
MendelianViolation: Some getter methods were added for chartl and VariantEval.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5447 348d0f76-0448-11de-a6fe-93d51630548a
b) small bug fix when setting debug arguments
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5446 348d0f76-0448-11de-a6fe-93d51630548a
ps: I moved it out of tribble. If you think it should reside in a different place, just yell at me.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5436 348d0f76-0448-11de-a6fe-93d51630548a
Reinstated. Proper unit test to follow.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5434 348d0f76-0448-11de-a6fe-93d51630548a
GenotypeAndValidate: now annotates the validations with callStatus.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5425 348d0f76-0448-11de-a6fe-93d51630548a
b) Add an experimental annotation to log indel type string inside the INFO field, just for debugging/temp analysis purposes (will consider making it standard if it proves useful).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5424 348d0f76-0448-11de-a6fe-93d51630548a
given an annotated VCF and a BAM file, it genotypes (using the reads in the BAM) each variant in the VCF (for snp or indel) and validates (or not) the 'known' annotation. Outputs a truth table with the PPV and NPV values, and optionally a vcf file with the variants that had enough coverage to be validated. You can optionally provide a minimum depth of coverage and only do the analysis conditional on that. (will write a wiki for this walker, as it might be useful for future validation essays).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5409 348d0f76-0448-11de-a6fe-93d51630548a
- Don't know how I got the wiggle header so utterly wrong. Fixed.
- Q-values now have a static maximum of 2000 so IGV averaging won't make everything look spikey and ugly.
- Changing windows to size 100 for (hopefully) better resolution.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5406 348d0f76-0448-11de-a6fe-93d51630548a
- Basic
- Multiple technology
- Test minIndelCnt parameter
Added also 2 disabled tests:
- Parallelization: issue w/code right now is that if -nt > 1, filter field shows "PASS" instead to ".", cause TBD
- Genotype given alleles mode: code not working yet.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5404 348d0f76-0448-11de-a6fe-93d51630548a
GAV: First version of the walker that validates reads from a BAM file based on an annotated VCF with TP/FP annotations.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5396 348d0f76-0448-11de-a6fe-93d51630548a
same shards as the previous sharder, so that I can directly compare filespans
to see where some performance bugs lie.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5395 348d0f76-0448-11de-a6fe-93d51630548a
-disc (--discordance) parameter together with a ROD track will output a VCF with the variants in the ROD track that are not present in the 'variants' VCF. Useful tool to list the variants from hapmap (for example) that weren't called in a dataset.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5392 348d0f76-0448-11de-a6fe-93d51630548a
Model is disabled by default and we're still using the old Dindel model until I'm more confident that new model is a definitive improvement, so right now this is enabled by hidden command line arguments, and it's not to be used yet.
In detail:
a) Several refactorings to share softMax() available to other modules, so its now part of MathUtils.
b) Refactored a couple of read utilities and moved from BAQ to ReadUtils.
c) New PairHMMIndelErrorModel class implementing new likelihood model
d) Several new hidden debug arguments in UAC.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5389 348d0f76-0448-11de-a6fe-93d51630548a
kshakir
chartl
hanna
delangel
carneiro
ebanks
depristo
kiran
asivache
fromer
corin
rpoplin