0439047269
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-27 10:49:45 -04:00
05b44dd017
The genotypeCounts array wasn't always being initialized before it was accessed, leading to a NPE (which got caught and thrown as a JEXL expression when used in selection). Added unit test to cover all genotype count methods.
2012-04-27 10:49:36 -04:00
9801dd114f
Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped
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The GATK -L unmapped is for GenomeLocs with SAMRecord.NO_ALIGNMENT_REFERENCE_NAME, not SAMRecord.getReadUnmappedFlag()
Previously unmapped flag reads in the last bin were being printed while also seeking for the reads without a reference contig.
2012-04-27 09:58:38 -04:00
2f86ccb086
Correct md5's for previous code change
2012-04-26 16:20:41 -04:00
972d6531b6
Corner case fix for indel GL computation: sometimes (depending on surrounding context) reads which are not informative of two candidate haplotypes end up having marginally higher likelihoods with one haplotype as opposed to another, depending on uncertainty on alignments in surrounding regions. So, a sample whose GL is -0.0001,-0.0005,-0.001 may have its genotype set to 1/1 due to this statistical noise. We already have a tolerance comparing max(gl)-min(gl) to avoid genotyping, so this tolerance is now increased from 0.001 to 0.1 (equivalent to 1 PL unit) to avoid genotyping a sample if all PLs are within this threshold. Changed 2 integration test md5s that hit this case.
2012-04-26 10:15:26 -04:00
ab2a952ad1
PED support for Inbreeding Coefficient annotation
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Signed-off-by: Eric Banks <ebanks@broadinstitute.org>
2012-04-25 12:56:47 -04:00
219b0a128b
PED support for ChromosomeCounts annotation
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Signed-off-by: Eric Banks <ebanks@broadinstitute.org>
2012-04-25 12:50:04 -04:00
19d5213d5a
Added function to get founders IDs in SampleDB
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Signed-off-by: Eric Banks <ebanks@broadinstitute.org>
2012-04-25 12:49:36 -04:00
dab25afc88
Add warning message about ratios in variantQCreport, give ratio for MAF > 10%
2012-04-25 12:22:32 -04:00
902277856e
fix for RBP getPileupsForSamples()
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do not differentiate per sample pileups from generic pileups. Do the same for both -- it's O(n) either way.
2012-04-24 17:20:30 -04:00
82b4798913
CountBasesWalker -- a quick QC walker.
2012-04-24 17:20:30 -04:00
e440d0ce69
BQSR triage #4
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* fixed queue script plot file names
* updated the ReadGroupCovariate to use the platform unit instead of sample + lane.
* fixed plotting of marginalized reported qualities
2012-04-24 17:19:54 -04:00
d6277b70d8
Forgot to consider the optimized case in hasAllele
2012-04-24 11:32:28 -04:00
91bad244d5
Using a VCF whose ALT is the reference in GGA mode is a User Error
2012-04-24 11:08:37 -04:00
74ad008163
Adding VariantContext.hasAlternateAllele functionality
2012-04-24 11:07:46 -04:00
66f3315548
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-24 09:39:55 -04:00
bcb93dda5f
Fixing docs (rank sum test values are not phred-scaled)
2012-04-24 09:39:42 -04:00
e39a59594a
BQSR triage and test routines
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* updated BQSR queue script for faster turnaround
* implemented plot generation for scatter/gatherered runs
* adjusted output file names to be cooperative with the queue script
* added the recalibration report file to the argument table in the report
* added ReadCovariates unit test -- guarantees that all the covariates are being generated for every base in the read
* added RecalibrationReport unit test -- guarantees the integrity of the delta tables
2012-04-23 11:23:00 -04:00
a733723439
Merged bug fix from Stable into Unstable
2012-04-23 10:30:30 -04:00
2761da975e
Handle null VCs (which can arise when indels are present in the file)
2012-04-23 10:30:00 -04:00
cd63bcb1b8
Fixing unit tests to register the user exception being thrown (instead of the NumberFormatException)
2012-04-23 10:06:51 -04:00
63aa79df82
Slightly better error message
2012-04-23 09:37:28 -04:00
7b5fbf9567
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-23 09:34:08 -04:00
4edb005411
Catch poorly formatted PL/GL fields
2012-04-23 09:33:50 -04:00
35bb55f562
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-22 13:23:36 -04:00
18e4532d10
Turning down the amount of assembly graph pruning slightly in the case of low coverage.
2012-04-22 13:23:24 -04:00
1f23d99dfa
If we are subsetting alleles in the UG (either because there were too many or because some were not polymorphic), then we may need to trim the alleles (because the original VariantContext may have had to pad at the end). Thanks to Ryan for reporting this. Only one of the integration tests had even partially covered this case, so I added one that did.
2012-04-20 17:00:05 -04:00
4b81c75642
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-20 14:30:19 -04:00
f1c5510ec0
When running SelectVariants with the excludeNonVariants option, remove alleles from the ALT field that are no longer polymorphic.
2012-04-20 14:30:04 -04:00
a1596791af
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-20 14:03:04 -04:00
a57295eb75
Fixing a bug when breaking up active regions where the resulting regions would overlap by one base. Adding quality score manipulation from the UG into the haplotype caller (qual capped by mapping quality, min qual threshold).
2012-04-20 14:02:55 -04:00
de68363c23
Removed experimental feature (aka hack) that was meant for 1000G consensus but remained in VQSR data manager - QD was being scaled by indel length. There's no evidence any more that QD is length-dependent, neither in CEU trio data nor in latest 1000G P2 calls
2012-04-20 10:58:34 -04:00
d2488dfb81
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-19 19:40:03 -04:00
c44c7b9a97
Restored optimization in Pair HMM only to compute HMM matrices starting in index where haplotypes start to diverge - saves about 15-20% of runtime which is what we lost by disabling banding in latest version, so runtime should be now about the same as what it was before refactoring. Output is bit-true to previous commit
2012-04-19 19:39:43 -04:00
0f8c77391d
BQSR bug triage #3
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* fixed context covariate famous "off by one" error
* reduced maximum quality score to Q50 (following Eric/Ryan's suggestion)
* remove context downsampling in BQSR R script
2012-04-19 17:31:04 -04:00
df5dd841af
AC strat now checks if evals will be merged before throwing an error on multiple eval files.
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Minor tweaks to WGP script based on new recal VCF format.
2012-04-19 16:08:55 -04:00
1ae2ab5b63
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-19 12:50:29 -04:00
0e6e0cb907
Merging bug fixes
2012-04-19 12:49:30 -04:00
79272c5e15
Thanks to Menachem for pointing out that the docs for genotyping_mode and output_mode were the same (and unclear). Fixed.
2012-04-19 12:48:09 -04:00
02ff930f6a
My changes
2012-04-19 12:45:18 -04:00
2485cef5b8
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-19 11:46:06 -04:00
76a6e37f4f
Don't output callability metrics by default anymore; one can still have them output to the 'metrics' file (which is now @Hidden because they are really for GSA use). Added a TODO to move UG from @By reference to reads and rods once LIBS is cleaned up.
2012-04-19 11:45:56 -04:00
1ea4e48a27
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-04-19 11:32:32 -04:00
11001ab9a2
Adding option to HaplotypeCaller to genotype the events on the chosen haplotypes as independent events. The filtered reads are now kept around so they can be passed to the variant annotations. Unfortunately the filtered reads aren't assigned a likelihood yet so they are all thrown in the Allele.NO_CALL bin.
2012-04-19 11:32:10 -04:00
eb22cd7222
Unit test to guarantee BQSR sequential calculation accuracy
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This test brings together the old and the new BQSR, building a recalibration table using the two separate frameworks and performing the recalibration calculation using the two different frameworks for 10,000+ bases and asserting that the calculations match in every case.
2012-04-19 09:33:40 -04:00
68d0211fa1
Improved BQSR plotting and some new parameters
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* Refactored CycleCovariate to be a fragment covariate instead of a per read covariate
* Refactored the CycleCovariateUnitTest to test the pairing information
* Updated BQSR Integration tests accordingly
* Made quantization levels parameter not hidden anymore
* Added hidden option to keep intermediate plotting files for debug purposes (they're automatically deleted)
* Added hidden option not to generate the plots automatically (important for scatter/gathering)
2012-04-19 09:31:41 -04:00
143e92b797
Rebasing
2012-04-18 20:05:43 -04:00
960e7e6aaf
Changes to integration tests
2012-04-18 19:53:42 -04:00
82efd4457e
Revert some bad merge changes
2012-04-18 16:35:09 -04:00
31c394d588
Resolve merge conflicts
2012-04-18 16:25:03 -04:00
Eric Banks
Khalid Shakir
Guillermo del Angel
Laurent Francioli
Mark DePristo
Mauricio Carneiro
Ryan Poplin