15c0c294c1
Adding in this walker to try to debug the 0-byte ref bases
2012-01-23 14:51:24 -05:00
02450e4b12
Merged bug fix from Stable into Unstable
2012-01-23 12:08:39 -05:00
798596257b
Enable the Genotype Phasing Evaluator. Because it didn't have the same argument structure as the base class, update2 of VariantEvaluator was being called, rather than update2 of the actual module.
2012-01-23 10:50:16 -05:00
80a4ce0edf
Bugfix for incorrect error messages for missing BAMs and VCFs
...
-- Missing BAMs were appearing as StingExceptions
-- Missing VCFs were showing up as CommandLineErrors, but it's clearer for them to be CouldNotReadInputFile exceptions
-- Added integration tests to ensure missing BAMs, VCFs, and -L files are properly thrown as CouldNotReadInputFile exceptions
-- Added path to standard b37 BAM to BaseTest
-- Cleaned up code in SAMDataSource, removing my parallel loading code as this just didn't prove to be useful.
2012-01-23 09:52:07 -05:00
31d2f04368
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-23 09:23:03 -05:00
966387ca0b
Next intermediate commit in the pool caller. Lots of bug fixes and now we can emit true vcf's with calls in discovery mode (still of unknown quality) - old validation mode is temporarily broken,will be fixed in next refactoring.
2012-01-23 09:22:31 -05:00
4a08e8ca6e
Minor tweaks to T2D-related qscripts. Replacing old md5s from the BeagleIntegrationTest. All differences boiled down either to the accounting of genotypes changed (./. --> 0/0 is no longer a "changed" genotype, and original genotypes that were ./. are represented as OG=. rather than OG=./. .)
...
This is somewhat of an arbitrary decision, and is negotiable. I could see treating
GT:PL ./.:.
differently from
GT:PL .:0,3,6
but am not sure the worth of doing so.
2012-01-23 08:25:34 -05:00
4d6312d4ea
HaplotypeCaller is now an ActiveRegionWalker.
2012-01-22 14:31:01 -05:00
3b1aad4f17
After a minor and abject freakout, alter the T2D script to seek out truth sensitivities between 80 and 100, rather than between 0.8 and 1. Also, don't consider a genotype "changed by beagle" if the initial genotype is a no-call.
2012-01-20 23:43:51 -05:00
9b4f6afa21
Alterations to scripts for better performance. Grid search now expands the sens/spec tradeoff (90 was far too aggressive against hapmap chr20), and 20 max gaussians was too many, and caused errors. For consensus genotypes: remember to gunzip the beagle outputs before converting to VCF. Also, beagle can in fact create 'null' alleles in certain circumstances. I'm not sure what exactly those circumstances are, but those sites should be ignored. When it does, all alleles apear to be set to null, so this should not affect the actual phasing in the output VCF.
2012-01-20 23:07:59 -05:00
f3564bbf43
Ugh. Darn intelliJ not telling me I was missing an import statement.
2012-01-20 13:25:11 -05:00
b902d778ca
.
2012-01-20 13:22:46 -05:00
7c6a9471e8
After ensuring MultiplyLikelihoods does what I want it to do, add a quick and simple integration test to ensure I don't break it.
2012-01-20 13:20:13 -05:00
e245cde47f
A new beagle script for generating a reference panel from lowpass, exome, and chip data. This is for T2D, but potentially useful.
2012-01-20 12:48:32 -05:00
a91dd5d137
Merge branch 'master' of ssh://tin.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable
2012-01-20 12:45:16 -05:00
3fe73f155c
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-20 12:44:22 -05:00
4b18786b5d
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-19 22:05:20 -05:00
ace9333068
Active 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.
2012-01-19 22:05:08 -05:00
cd38110b7b
GQs are not always purged with this method of modifying attributes. To drop them, create the Genotype anew.
2012-01-19 20:11:20 -05:00
b9f7103d09
Fix edge case where DP annotations (format) were creeping in
2012-01-19 19:41:43 -05:00
72cd0a2450
And do it conditional on having likelihoods in the first place
2012-01-19 18:52:06 -05:00
ed5302667b
Oops. Let's actually retain the genotype likelihoods.
2012-01-19 18:44:39 -05:00
0644b75089
Remove attribute data from VariantContext and genotypes.
2012-01-19 18:30:32 -05:00
fda29ebcbd
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-19 18:22:04 -05:00
253d6483e1
Updated 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
2012-01-19 18:21:22 -05:00
066da80a3d
Added KEEP_UNCONDTIONAL option which permits even sites with only filtered records to be included as unfiltered sites in the output
2012-01-19 18:19:58 -05:00
6e30d715cf
Minor changes to T2D VQSR. Adding in a small walker for multiplying likelihoods for generation of a consensus panel.
2012-01-19 18:00:07 -05:00
ced6775de3
Changes to allow for external tests
...
Changes to the build script that allow the external directory to have tests.
This means groups like CGA don't have to reinvent the wheel on testing, and
can instead use the GATKs unit and integration tests.
Signed-off-by: David Roazen <droazen@broadinstitute.org>
2012-01-19 13:04:24 -05:00
98f8431b07
Right. Forgot the = true. If only there were some way to silently commit this OH WAIT
2012-01-19 12:36:30 -05:00
7f3ad25b01
Adding a mode to VariantFiltration to invalidate previously-applied filters to allow complete re-filtering of a VCF.
...
T2D VQSR: re-calling now done with appropriate quality settings and using BAQ.
2012-01-19 10:54:48 -05:00
ecdd07b748
updating HaplotypeCaller integration test
2012-01-19 09:31:22 -05:00
7e082c7750
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-19 09:11:23 -05:00
d1c8c38541
A QScript to generate a VQSR of union sites for T2D, using a broad set and a union site set as input.
2012-01-19 02:04:04 -05:00
39e6df5aa9
Fix edge case for very small VCFs
2012-01-19 00:51:28 -05:00
1e037a0ecf
Ensure second-to-last line printed
2012-01-19 00:33:08 -05:00
9946853039
Remove duplicated line
2012-01-19 00:25:22 -05:00
cf9b1d350a
Some minor changes to in-process functions that nobody else uses. CGL now properly ignores no-calls for external VCFs.
2012-01-19 00:20:49 -05:00
ab8f499bc3
Annotate with FS even for filtered sites
2012-01-18 22:04:51 -05:00
b0b0cd9aef
Conforming to the guru's recommendation on library usage ;-)
...
thanks Khalid.
2012-01-18 21:19:16 -05:00
b123416c4c
Resolve stale merge changes
2012-01-18 20:56:36 -05:00
2eb45340e1
Initial, 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
2012-01-18 20:54:10 -05:00
0133d1a901
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-18 09:53:42 -05:00
0268da7560
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-18 09:53:00 -05:00
60024e0d7b
updating TDT integration test
2012-01-18 09:52:50 -05:00
b7c65cb089
Merged bug fix from Stable into Unstable
2012-01-18 09:52:47 -05:00
11982b5a34
We 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.
2012-01-18 09:42:41 -05:00
ca11f68303
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-18 08:29:03 -05:00
9e77facda5
More analyses for random forest test script forest.R
2012-01-18 08:28:47 -05:00
5bd1a45879
Usability improvements to analyzeRunReports
...
-- Print out the name / db of SQL server, not a python connection object
-- Print out the ID, not a python objects, of XML record that fails to convert
2012-01-18 08:27:15 -05:00
b52db51599
Don't try to write log to a non-existant file
2012-01-18 08:26:49 -05:00
Christopher Hartl
Mark DePristo
Guillermo del Angel
Ryan Poplin
Menachem Fromer
Aaron McKenna
Eric Banks
Mauricio Carneiro
David Roazen