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.
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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
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-- 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
763c81d520
No longer enforce MAX_ALLELE_SIZE in VCF codec
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-- Instead issue a warning when a large (>1MB) record is encountered
-- Optimized ref.getBytes()[i] => (byte)ref.charAt(i), which avoids an implicit O(n) allocation each iteration through computeReverseClipping()
2012-01-18 07:35:11 -05:00
0c7865fdb5
UnitTest for reverseAlleleClipping
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-- No code modified yet, just implementing a unit test to ensure correctness of the existing code
2012-01-18 07:35:11 -05:00
d5199db8ec
Be explicit about setting the snpEff -onlyCoding option in the pipeline
...
When run without an explicit -onlyCoding option, as we've been doing up to
now, snpEff automatically sets -onlyCoding to "true" provided that there is
at least one transcript marked as "protein_coding", which will always be the
case for us in practice (and indeed, all pipeline runs so far with snpEff
2.0.5 have run with -onlyCoding auto-set to "true").
However, given the disastrous effect on annotation quality setting
"-onlyCoding false" has, we wish to be explicit with this option
rather than relying on snpEff's auto-detection logic.
2012-01-17 20:04:27 -05:00
9770250b72
Fix for Amy W - evidently binding defaults are not null but an unbound object, which caused the improper branch to be entered into.
2012-01-17 17:28:58 -05:00
b0560f9440
Rev. tribble to fix BED codec bug in tribble 51
2012-01-17 16:40:26 -05:00
62801e430a
Bugfix for unnecessary optimization
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-- don't cache the ref bytes
2012-01-17 16:40:26 -05:00
f2b0575dee
Detect unreasonably large allele strings (>2^16) and throw an error
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-- samtools can emit alleles where the ref is 42M Ns and this caused the GATK (via tribble) to hang in several places.
-- Tribble was updated so we actually could read the line properly (rev. to 51 here).
-- Still the parsing algorithms in the GATK aren't happy with such a long allele. Instead of optimizing the code around an improper use case I put in a limit of 2^16 bp for any allele, and throw a meaningful exception when encountered.
2012-01-17 16:40:26 -05:00
816dcf9616
Finally got around to adding support for Eric's fix to permit annotation exclusion by VariantAnnotator
2012-01-17 16:35:16 -05:00
8b0ddf0aaf
Adding notes to CountCovariates docs about using interval lists as database of known variation
2012-01-17 16:13:13 -05:00
ff2fc514ae
Updated plots to CGL walker
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a few updates on the CalibrateGenotypeLikelihoods walker output
* Fixed ggplot2 issue with dataset with poor coverage
* Added jitter as default geometry
* Dropped the cut by technology from the graphs
2012-01-17 15:14:47 -05:00
56761297dd
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-17 15:03:32 -05:00
75f87db468
Replacing Mills file with new gold standard indel set in the resource bundle for release with v1.5
2012-01-17 15:02:45 -05:00
40ebc17437
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-17 14:49:17 -05:00
41d70abe4e
At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.
2012-01-17 14:47:53 -05:00
2390449f0f
Local and S3 archiving scripts now push data to MySQL as well
2012-01-17 14:42:48 -05:00
ae259f81cc
Bug fixing for merging of read fragments when one fragment contained an indel
2012-01-17 14:39:27 -05:00
Ryan Poplin
Christopher Hartl
Menachem Fromer
Aaron McKenna
Eric Banks
Mauricio Carneiro
Guillermo del Angel
David Roazen
Mark DePristo
Matt Hanna