Using samtools to merge the low pass bams before cleaning to avoid "Too many open files." with 1500+ bams.
Other minor cleanup as pointed out by the IntelliJ scala plugin.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5942 348d0f76-0448-11de-a6fe-93d51630548a
a) Genotype given alleles with indels
b) Genotyping and computing likelihoods of multi-allelic sites.
When GGA option is enabled, indels will be called on regular pileups, not on extended pileups (extended pileups will be removed shortly in a next iteration). As a result, likelihood computation is suboptimal since we can't see reads that start with an insertion right after a position, and hence quality of some insertions is removed and we could be missing a few marginal calls, but it makes everything else much simpler.
For multiallelic sites, we currently can't call them in discovery mode but we can genotype them and compute/report full PL's on them (annotation support comes in next commit). There are several suboptimal approximations made in exact model to compute this. Ideally, joint likelihood Pr(Data | AC1=i,AC2=j..) should be computed but this is hard. Instead, marginal likelihoods are computed Pr(Data | ACi=k) for all i,k, and QUAL is based on highest likelihood allele.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5941 348d0f76-0448-11de-a6fe-93d51630548a
Upped the WGP VQSR memory to 32g to power through the filtering whole genome. TODO: Figure out what the right amount is.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5940 348d0f76-0448-11de-a6fe-93d51630548a
caveat: Right now bwa only supports one read group, so if the original file had multiple @RG lines, only the first one will be kept. (working on a solution to this)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5931 348d0f76-0448-11de-a6fe-93d51630548a
Renamed it and moved to core. Happy to support it.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5930 348d0f76-0448-11de-a6fe-93d51630548a
- Verified that exact calculations do agree with R's dwilcox()
- Verified that exact calculations do not agree with R's wilcox.test
+ This is because R does a correction, and calculates CDFs rather than PDFs (e.g. sums over dwilcox() values)
- Can now specify MWU to calculate cumulative exact tests, rather than point probabilities
- Z-scores are now calculated properly for exact tests
+ Previously, z-values calculated by inverting normal CDF from U-statistic PDF
+ Now both inversions are done, with a smart heuristic (biased variance) to make the point-calculated Z-value more accurate
+ Additional tests
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5911 348d0f76-0448-11de-a6fe-93d51630548a
continue to exist and live in playground (and thus outside of the normal release
/ git release branch).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5909 348d0f76-0448-11de-a6fe-93d51630548a
ReplicationValidationWalker: Just the skeleton of what will be the implementation of the replication/validation model.
dataProcessingV2: Committing an UNTESTED implementation of BWA alignment. I am running tests on it over the weekend.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5900 348d0f76-0448-11de-a6fe-93d51630548a
Current tribble-129M.jar in SVN does not work with current version of GATK code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5897 348d0f76-0448-11de-a6fe-93d51630548a
IndelRealignerIntegrationTest failures -- yes, it's the classic printf()
debugging technique. Will revert in a day or two once I get the data I need :)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5896 348d0f76-0448-11de-a6fe-93d51630548a
1. findGenes : Parses the Genetic Association Database (from NIH) into an annotated 'genes of interest' interval_list file.
2. sortGenesByCoverage : combines the interval_list of the genes of interest with the report from GATK's DepthOfCoverage, generating an annotated interval_list with total and average coverages on each gene.
3. hasTheseTargets : Give it a list of targets (example: exon targets) and any interval_list (example: genes of interest) and it will generate an annotated interval_list of all the exons that are contained in the list of genes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5894 348d0f76-0448-11de-a6fe-93d51630548a
kshakir
delangel
depristo
ebanks
fromer
carneiro
chartl
droazen
rpoplin
hanna
kiran