e245cde47fA new beagle script for generating a reference panel from lowpass, exome, and chip data. This is for T2D, but potentially useful.
Christopher Hartl
2012-01-20 12:48:32 -0500
a91dd5d137Merge branch 'master' of ssh://tin.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable
Christopher Hartl
2012-01-20 12:45:16 -0500
3fe73f155cMerge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Christopher Hartl
2012-01-20 12:44:22 -0500
4b18786b5dMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-01-19 22:05:20 -0500
ace9333068Active region walkers can now see the reads in a buffer around thier active reigons. This buffer size is specified as a walker annotation. Intervals are internally extended by this buffer size so that the extra reads make their way through the traversal engine but the walker author only needs to see the original interval. Also, several corner case bug fixes in active region traversal.
Ryan Poplin
2012-01-19 22:05:08 -0500
cd38110b7bGQs are not always purged with this method of modifying attributes. To drop them, create the Genotype anew.
Christopher Hartl
2012-01-19 20:11:20 -0500
b9f7103d09Fix edge case where DP annotations (format) were creeping in
Christopher Hartl
2012-01-19 19:41:43 -0500
72cd0a2450And do it conditional on having likelihoods in the first place
Christopher Hartl
2012-01-19 18:52:06 -0500
ed5302667bOops. Let's actually retain the genotype likelihoods.
Christopher Hartl
2012-01-19 18:44:39 -0500
0644b75089Remove attribute data from VariantContext and genotypes.
Christopher Hartl
2012-01-19 18:30:32 -0500
fda29ebcbdMerge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Menachem Fromer
2012-01-19 18:22:04 -0500
253d6483e1Updated Batch-merge to retain ALL sites in input (SNPs, indels, regardless of their filtering status), and also optionally go back to the BAMs to perform VariantAnnotation
Menachem Fromer
2012-01-19 18:21:22 -0500
066da80a3dAdded KEEP_UNCONDTIONAL option which permits even sites with only filtered records to be included as unfiltered sites in the output
Menachem Fromer
2012-01-19 18:19:58 -0500
6e30d715cfMinor changes to T2D VQSR. Adding in a small walker for multiplying likelihoods for generation of a consensus panel.
Christopher Hartl
2012-01-19 15:01:50 -0500
ced6775de3Changes to allow for external tests
Aaron McKenna
2012-01-18 16:34:42 -0500
98f8431b07Right. Forgot the = true. If only there were some way to silently commit this OH WAIT
Christopher Hartl
2012-01-19 12:36:30 -0500
7f3ad25b01Adding a mode to VariantFiltration to invalidate previously-applied filters to allow complete re-filtering of a VCF.
Christopher Hartl
2012-01-19 10:54:48 -0500
ecdd07b748updating HaplotypeCaller integration test
Ryan Poplin
2012-01-19 09:31:22 -0500
7e082c7750Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-01-19 09:11:23 -0500
d1c8c38541A QScript to generate a VQSR of union sites for T2D, using a broad set and a union site set as input.
Christopher Hartl
2012-01-19 02:04:04 -0500
39e6df5aa9Fix edge case for very small VCFs
Christopher Hartl
2012-01-19 00:51:28 -0500
1e037a0ecfEnsure second-to-last line printed
Christopher Hartl
2012-01-19 00:33:08 -0500
9946853039Remove duplicated line
Christopher Hartl
2012-01-19 00:25:22 -0500
cf9b1d350aSome minor changes to in-process functions that nobody else uses. CGL now properly ignores no-calls for external VCFs.
Christopher Hartl
2012-01-19 00:20:49 -0500
ab8f499bc3Annotate with FS even for filtered sites
Eric Banks
2012-01-18 22:04:51 -0500
b0b0cd9aefConforming to the guru's recommendation on library usage ;-)
Mauricio Carneiro
2012-01-14 21:58:49 -0500
b123416c4cResolve stale merge changes
Guillermo del Angel
2012-01-18 20:56:36 -0500
2eb45340e1Initial, raw, mostly untested version of new pool caller that also does allele discovery. Still needs debugging/refining. Main modification is that there is a new operation mode, set by argument -ALLELE_DISCOVERY_MODE, which if true will determine optimal alt allele at each computable site and will compute AC distribution on it. Current implementation is not working yet if there's more than one pool and it will only output biallelic sites, no functionality for true multi-allelics yet
Guillermo del Angel
2012-01-18 20:54:10 -0500
0133d1a901Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-01-18 09:53:42 -0500
0268da7560Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-01-18 09:53:00 -0500
60024e0d7bupdating TDT integration test
Ryan Poplin
2012-01-18 09:52:50 -0500
b7c65cb089Merged bug fix from Stable into Unstable
David Roazen
2012-01-18 09:52:47 -0500
11982b5a34We no longer calculate the population-level TDT statistic if there are fewer than 5 trios with full genotype likelihood information. When there is a high degree of missingness the results are skewed or in the worst case come out as NaN.
Ryan Poplin
2012-01-18 09:42:41 -0500
ca11f68303Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Mark DePristo
2012-01-18 08:29:03 -0500
9e77facda5More analyses for random forest test script forest.R
Mark DePristo
2012-01-18 08:28:47 -0500
5bd1a45879Usability improvements to analyzeRunReports
Mark DePristo
2012-01-18 08:27:15 -0500
b52db51599Don't try to write log to a non-existant file
Mark DePristo
2012-01-18 08:26:49 -0500
763c81d520No longer enforce MAX_ALLELE_SIZE in VCF codec
Mark DePristo
2012-01-17 21:06:02 -0500
0c7865fdb5UnitTest for reverseAlleleClipping
Mark DePristo
2012-01-17 19:18:04 -0500
d5199db8ecBe explicit about setting the snpEff -onlyCoding option in the pipeline
David Roazen
2012-01-17 16:26:16 -0500
9770250b72Fix for Amy W - evidently binding defaults are not null but an unbound object, which caused the improper branch to be entered into.
Christopher Hartl
2012-01-17 17:28:58 -0500
b0560f9440Rev. tribble to fix BED codec bug in tribble 51
Mark DePristo
2012-01-17 15:56:49 -0500
62801e430aBugfix for unnecessary optimization
Mark DePristo
2012-01-16 18:49:58 -0500
f2b0575deeDetect unreasonably large allele strings (>2^16) and throw an error
Mark DePristo
2012-01-16 14:07:42 -0500
816dcf9616Finally got around to adding support for Eric's fix to permit annotation exclusion by VariantAnnotator
Menachem Fromer
2012-01-17 16:35:16 -0500
8b0ddf0aafAdding notes to CountCovariates docs about using interval lists as database of known variation
Ryan Poplin
2012-01-17 16:13:13 -0500
ff2fc514aeUpdated plots to CGL walker
Mauricio Carneiro
2012-01-17 15:12:49 -0500
56761297ddMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-01-17 15:03:32 -0500
75f87db468Replacing Mills file with new gold standard indel set in the resource bundle for release with v1.5
Ryan Poplin
2012-01-17 15:02:45 -0500
40ebc17437Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
Matt Hanna
2012-01-17 14:49:17 -0500
41d70abe4eAt chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.
Matt Hanna
2012-01-17 14:47:53 -0500
2390449f0fLocal and S3 archiving scripts now push data to MySQL as well
Mark DePristo
2012-01-17 14:42:48 -0500
ae259f81ccBug fixing for merging of read fragments when one fragment contained an indel
Ryan Poplin
2012-01-17 14:39:27 -0500
80a1ae254bMerge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Menachem Fromer
2012-01-17 14:25:40 -0500
284a8e9ddcFixed to match recent minor updates by Khalid and Eric
Menachem Fromer
2012-01-17 14:24:41 -0500
cde224746fBait Redesign supports baits that overlap, by picking only the start of intervals.
Christopher Hartl
2012-01-17 13:51:05 -0500
8e23c98dd9Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-01-17 13:46:28 -0500
32ccde374bMerged bug fix from Stable into Unstable
Matt Hanna
2012-01-17 11:08:35 -0500
3ba918aff1Error message cleanup in BAM indexing code.
Matt Hanna
2012-01-17 11:05:42 -0500
aa8a885a5bGeneralizing forest.R analysis script
Mark DePristo
2012-01-16 09:33:41 -0500
8ddac9a06fDon't show individual jobs in queueStatus for gsaadm, just count
Mark DePristo
2012-01-16 09:33:05 -0500
61f82f138fExtract a high-level GATK version from the SVN / GIT full version numbers in analyzeRunReports
Mark DePristo
2012-01-16 09:30:48 -0500
8272c8bd26Added exceptions to CGL walker
Mauricio Carneiro
2012-01-14 14:10:19 -0500
cec7107762Better location for the downsampling of reads in PrintReads
Mauricio Carneiro
2012-01-14 12:13:15 -0500
3a9d9789aeRemoving old scripts for genotype accuracy
Mauricio Carneiro
2012-01-13 16:56:57 -0500
ca48f04fb8Better handling in pre QC R scripts for older projects (whole_exome_agilent_designed_120) that came out before some metrics were added to Picard. PCT_PF_READS was plotted with a plot title for PCT_PF_ALIGNED_READS. Now plotting both metrics separately.
Khalid Shakir
2012-01-13 16:30:04 -0500
b06074d6e7Updated SortingVCFWriterBase to use PriorityBlockingQueue so that the class is thread-safe
Mark DePristo
2012-01-13 09:24:13 -0500
2c3176eb80Merged bug fix from Stable into Unstable
Matt Hanna
2012-01-12 13:31:10 -0500
cd43f016ceFixed NPE in getNextOverlappingBAMScheduleEntry() when mixed mapped/unmapped interval lists are used. Added integrationtest to verify behavior.
Matt Hanna
2012-01-12 13:29:11 -0500
ed34b4f088Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-01-12 10:27:26 -0500
e7fe9910f7Create the temp storage for calculating cell values just once as per Mark's TODO
Eric Banks
2012-01-12 10:27:10 -0500
f5f5ed5dcdDon't initialize the cell conformation values (use an else in the loop instead) as per Mark's TODO
Eric Banks
2012-01-12 08:50:03 -0500
410a340ef5Swapping the iteration order to run over AF conformations and then samples instead of the reverse minimizes calls to HashMap.get; instead of it being O(n) since we called it for each sample it's now O(1). Runtime on T2D GENES test set is reduced by 5-10%. More optimizations to follow.
Eric Banks
2012-01-12 02:04:03 -0500
423d4ac2d3Quick fix to CalibrateGenotypeLikelihoods
Mauricio Carneiro
2012-01-11 17:47:08 -0500
77a03c9709Patching special case in the adaptor clipping
Mauricio Carneiro
2012-01-10 16:30:38 -0500
34cf2fe43bMerged bug fix from Stable into Unstable
Mark DePristo
2012-01-11 08:55:20 -0500
2e47336a81Only print out error report for most recent release in runGATKReport.py
Mark DePristo
2012-01-11 08:54:17 -0500
aae61767c6queueJobReport now compresses PDF when running R 2.13+. Updated PostCallingQC.scala's VE and R to include missense to silent ratio and plot.
Khalid Shakir
2012-01-10 17:32:30 -0500
a9a6516527Merged bug fix from Stable into Unstable
Khalid Shakir
2012-01-10 16:16:10 -0500
ef50e77ee2When running Queue jobs locally, merge the stderr to the stdout log if the error file is NOT specified. Updated VE strats in the HSP for plotting Ka/Ks by AC.
Khalid Shakir
2012-01-10 16:10:25 -0500
3475bfafd3Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-01-10 12:39:15 -0500
5bf960deb8adding dbsnp to indel VQSR
Mauricio Carneiro
2012-01-10 12:38:35 -0500
25d0d53d88Moving the approximate summing of log10 vals to MathUtils; keeping the more efficient implementation of fast rounding.
Eric Banks
2012-01-10 12:38:47 -0500
589397d611Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-01-10 12:36:48 -0500
c5320ef1afResolving changes in integration test during merge
Eric Banks
2012-01-10 12:14:16 -0500
e923a2e512Revving Picard to incorporate final version of ReadWalker performance improvements.
Matt Hanna
2012-01-10 12:12:33 -0500
0f36f6947eResolving merge conflicts
Eric Banks
2012-01-10 11:44:16 -0500
f2cecce10fMuch better implementation of the approximate summing of an array of log10 values (including more efficient rounding). Now effectively takes 0% of UG runtime on T2D GENES (as opposed to 11% previously).
Eric Banks
2012-01-10 11:34:23 -0500
509c3d87b0Merged bug fix from Stable into Unstable
Matt Hanna
2012-01-09 23:08:46 -0500
dc60757b68Eliminate unnecessary strong references (and therefore memory held) by tree reduce entries that have already been processed.
Matt Hanna
2012-01-09 23:04:53 -0500
4c3c93fc92Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Menachem Fromer
2012-01-09 18:18:09 -0500
133739a76eAdd option to run the longer components on a different queue
Menachem Fromer
2012-01-09 18:17:39 -0500
6b9dcaf979added a -o option to AssessLikelihoodsAtTruth
Mauricio Carneiro
2012-01-09 16:53:48 -0500
6f2abd76dfUpdating the MDCP with the new indel gold standard from Ryan.
Mauricio Carneiro
2012-01-09 15:31:18 -0500
f01f7d1db8Merged bug fix from Stable into Unstable
Mark DePristo
2012-01-09 08:41:14 -0500
845c0b1c66Merge branch 'master' of ssh://depristo@gsa1/humgen/gsa-scr1/gsa-engineering/git/stable
Mark DePristo
2012-01-09 08:40:59 -0500
f5add25c72Improved formatting of queueStatus
Mark DePristo
2012-01-09 08:40:53 -0500
fda1795791Merged bug fix from Stable into Unstable
Matt Hanna
2012-01-08 22:04:44 -0500
Christopher Hartl
Ryan Poplin
Menachem Fromer
Aaron McKenna
Eric Banks
Mauricio Carneiro
Guillermo del Angel
David Roazen
Mark DePristo
Matt Hanna
Khalid Shakir