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Author SHA1 Message Date
Laura Gauthier f7eb5d3082 Enable family-level stratification (if a ped file is provided) 2015-10-28 09:55:04 -04:00
Laura Gauthier 68a2f1243d Finished draft of code for new map-combine-reduce annotation framework 
All VQSR annotations can be generated in allele-specific mode
Pull out allele-specific annotations in AS_Standard annotation group
 2015-10-27 09:44:49 -04:00
Laura Gauthier fcaf37279c Finished draft of code for new map-combine-reduce annotation framework 
All VQSR annotations can be generated in allele-specific mode
Pull out allele-specific annotations in AS_Standard annotation group
 2015-10-27 09:23:29 -04:00
Ron Levine 36ca9fe898 Allow LeftAlignAndTrimVariants to handle alleles longer than the default processing window 2015-10-25 20:33:56 -04:00
Ron Levine 795fe75886 Update doc for multiallelics, trimming is the default behavior 2015-10-22 04:04:09 -04:00
Takuto Sato df7a482335 VariantAnnotator now supports annotating FILTER field from an external resource. 
Updated the docs.
 2015-10-14 14:26:21 -04:00
Ron Levine 2bcded11cb VariantAnnotator checks alleles when annotationg with external resource 2015-10-08 17:01:30 -04:00
Eric Banks 622ec352bb Fix for combining records in which one has a spanning deletion and needs a padded reference allele. 
This was erroring out and not working.
 2015-10-02 16:28:16 -04:00
Kate Noblett 506958a0b7 Implemented a new VariantEval evaulation module, MetricsCollection. Fixed null pointer exception, updated tests. 2015-09-30 17:21:30 -04:00
Ron Levine 792142ec50 Implement BaseCounts per-sample 2015-09-30 08:59:11 -04:00
Samuel Lee c7f76b945e addressing PR comments 2015-09-24 15:42:51 -04:00
Samuel Lee 0dacf60012 Changed calls for RGQ=0 from 0/0 to ./. in output of GenotypeGVCFs. 2015-09-23 15:35:09 -04:00
Ron Levine 3ecabf7e45 Allow overriding ValidateVariants' hard-coded cutoff for allele length 2015-09-17 10:49:14 -04:00
meganshand 2507bf8d17 Fixed 7-PL genotypes in InbreedingCoeff tests 2015-09-14 12:00:45 -04:00
meganshand d767e1722e Excess Het P-value 
Added input exception

Added header line

Updated MD5s

Changing more MD5s

Made edge case clearer

Fixed formatting

Changed mid-point to mode
 2015-09-14 12:00:44 -04:00
Laura Gauthier 53b506a0b8 Make sure inputPriors get used if they are specified 
Fix usage of AF prior (i.e. theta) in probability of non-reference calculation
Refactored duplicate functions
Updated docs for heterozygosity
 2015-09-10 10:08:03 -04:00
Ron Levine 83a7012d69 Mask snps with --snpmask 2015-09-09 16:20:48 -04:00
Ron Levine 29ac64f6ce Calculate GenotypeAnnotations before InfoFieldAnnotations 2015-09-03 09:22:46 -04:00
Samuel Lee 41256e1405 Added file-extension--dependent interval-list output to RealignerTargetCreator. 2015-08-31 11:22:18 -04:00
Mark Fleharty daeb55429e Adding Static Binning to BQSR 2015-08-24 13:36:17 -04:00
Ron Levine 2afe3f7a21 Make GenotypeGVCFs subset Strand Allele Counts intelligently 2015-08-22 08:33:09 -04:00
Ron Levine beec624a63 Move htsjdk & picard to rev 1.138 2015-08-20 10:42:25 -04:00
Geraldine Van der Auwera 19bbe45cbc Updated licenses for 2015 2015-08-06 15:23:11 -04:00
David Benjamin 5fcc3788bd UnifiedGenotypingEngine queries VariantContext for model if not given 2015-08-05 15:30:37 -04:00
Eric Banks df033f674d Patch for the incorrect "fixing" of mates when supplementary alignments are present. 
Note that this patch involves ignoring supplementary alignments.  Ideally we would want
to fix their mates properly but that would require a major refactoring of this soon-to-be
deprecated tool.
 2015-08-05 12:55:39 -04:00
Louis Bergelson 9d9827f176 Merge pull request #1031 from broadinstitute/lb_update_for_java8 
Updated gatk so it compiles with java 8
 2015-07-28 11:09:19 -04:00
Geraldine Van der Auwera 5939b4c100 Merge pull request #1073 from broadinstitute/ldg_SV-MVtestNameFix 
Fix logging name on SelectVariantsIntegrationTest::testInvertMendelia…
 2015-07-27 16:54:59 -04:00
vruano 047aea9707 Address performance issue #1077 2015-07-23 13:44:10 -04:00
Laura Gauthier 4fefedfb0b Fix logging name on SelectVariantsIntegrationTest::testInvertMendelianViolationSelection() 2015-07-23 09:48:15 -04:00
Valentin Ruano Rubio 66cf22b28f Merge pull request #1069 from broadinstitute/vrr_ad_genotype_gvcfs_bugfix 
Fix AD propagation when subsetting alleles in non-diploid GenotypeGVCF.
 2015-07-22 18:53:43 -04:00
vruano 315e193e51 Fix AD propagation when subsetting alleles in non-diploid GenotypeGVCF. 
Addresses issue #913.

Also remove some commented out code and toxic debugging code that uses System.out/err.println.
 2015-07-22 17:08:13 -04:00
Joseph White 3bd988825f Removed walkers for handling Beagle data 
Added deprecation statements to DeprecatedToolChecks.java
    Removed integration test for Beagle walker
    Added URL for Beagle documentation
 2015-07-21 18:36:08 -04:00
Valentin Ruano Rubio 9360e1d293 Merge pull request #1059 from broadinstitute/vrr_true_false_list_removal 
More efficient implementation of the indel read qualities recalculati…
 2015-07-21 17:13:45 -04:00
vruano 82f1236633 More efficient implementation of the indel read qualities recalculation for the PCR error model. 
Addresses #1054.
 2015-07-21 14:25:11 -04:00
Ron Levine 6e46b3696e Merge contiguous intervals properly 2015-07-14 15:23:37 -04:00
Geraldine Van der Auwera c109a953f8 Merge pull request #1029 from broadinstitute/rhl_vqslod_definition 
Make VQSLOD definition accurate
 2015-07-06 19:52:15 -04:00
Ron Levine 1a7e83fa50 Merge if both GT are phased 2015-06-30 13:03:16 -04:00
Eric Banks f994220617 Update the allele remapping code to handle the new spanning deletion allele. 
Now that Ron updated the GATK so that we use star to represent spanning
deletions, we need to catch those cases in the code that remaps alleles.
Otherwise, we try to pad the stars and that's just bad.

Added test from actual failing data.
 2015-06-29 17:58:22 -04:00
Louis Bergelson e1c41b2c38 Updated gatk so it compiles on java 8 
updated cofoja to 1.2 from 1.0
added explicit type casts in places that java 8 required them
 2015-06-26 15:59:46 -04:00
Ron Levine 09686f4595 Make VQSLOD definition accurate 2015-06-25 16:47:50 -04:00
Geraldine Van der Auwera 719bb15340 Merge pull request #1019 from broadinstitute/rhl_var_index_param_gz 
Indexing parameters not required if output file has the g.vcf.gz exte…
 2015-06-17 14:30:20 -04:00
Geraldine Van der Auwera 697c4b0cf1 Added else clause to handle symbolic alleles 
Add test for createAlleleMapping
 2015-06-17 10:52:56 -04:00
Eric Banks fe0b5e0fbe Handle cases where a given sample has multiple spanning deletions. 
When a sample has multiple spanning deletions and we are asked to assign
likelihoods to the spanning deletion allele, we currently choose the first
deletion.  Valentin pointed out that this isn't desired behavior.  I
promised Valentin that I would address this issue, so here it is.

I do not believe that the correct thing to do is to sum the likelihoods
over all spanning deletions (I came up with problematic cases where this
breaks down).

So instead I'm using a simple heuristic approach: using the hom alt PLs, find
the most likely spanning deletion for this position and use its likelihoods.

In the 10K-sample VCF from Monkol there were only 2 cases that this problem
popped up.  In both cases the heuristic approach works well.
 2015-06-16 12:20:43 -04:00
Ron Levine b35085ca28 Indexing parameters not required if output file has the g.vcf.gz extensionv 2015-06-13 11:46:56 -04:00
Ron Levine dbed660183 Add spannning deletions allele 2015-06-12 16:43:06 -04:00
Ron Levine a6ca97ef14 Site-level selection based on genotype filter status 2015-05-21 11:27:20 -04:00
David Roazen caafe84e74 Rev htsjdk to version 1.132 and picard to version 1.131, and switch to using the versions in maven central 
-We now pull htsjdk and picard from maven central.

-Updated the GATK codebase as necessary to adapt to changes in the Feature
 interface.

-Since VCFHeader now requires that all header lines have unique keys, uniquified
 the keys of GVCFBlock header lines by including the min/max GQ in the key.
 Updated MD5s accordingly.

-Other MD5s changed as a result of an htsjdk fix to eliminate "-0" in VCF output.
 2015-05-14 15:26:23 -04:00
Geraldine Van der Auwera f6b3d8e862 Merge pull request #947 from broadinstitute/rhl_invert_selection 
Added --invert_selection flag for variant selection queries
 2015-05-13 13:40:32 -04:00
Eric Banks c752b9bca6 Fixed a small feature/bug that I introduced with the spanning deletions genotyping. 
In the case where there's a low quality SNP under a spanning deletion in the gvcfs:
if the SNP is not genotyped by GenotypeGVCFs (because it's just noise) we were still
emitting a record with just the symbolic DEL allele (because that allele is high quality).

We no longer do that.
 2015-05-13 11:19:40 -04:00
Ron Levine 4a75d54e65 Added invert and exclude flags for variant selection queries 2015-05-12 15:08:28 -04:00