09ac3779d6
Added ReadLikelihoods component to substitute Map<String,PerReadAlleleLikelihoodMap>.
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It uses a more efficient java array[] based implementation and encapsulates operations perform with such a
read-likelihood collection such as marginalization, filtering by position, poor modeling or capping
worst likelihoods and so forth.
Stories:
https://www.pivotaltracker.com/story/show/70222086
https://www.pivotaltracker.com/story/show/67961652
2014-08-11 17:46:28 -04:00
c56e493f98
Merge pull request #622 from broadinstitute/ldg_SORanalysis
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Add StrandOddsRatio to default annotations produced by GenotypeGVCFs
2014-08-11 09:45:27 -04:00
abcaba4bc3
Merge pull request #699 from broadinstitute/tf_hc_block_ranges
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Changed the default GVCF Q Bands from 5,20,60 to be 1..60 by 1s, 60...90...
2014-08-08 16:10:23 -04:00
5695f22da8
Changed the default GVCF Q Bands from 5,20,60 to be 1..60 by 1s, 60...90 by 10s and 99 in order to give finer resolution
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for homref PLs and ADs at lower confidences and somewhat higher resolution at higher confidences.
2014-08-08 14:31:35 -04:00
35de598e4b
Modify StrandOddsRatio calculation to take on lower values in cases where reference +/- reads are skewed but alt reads are not. Add SOR to default annotations produced by GenotypeGVCFs. Add jitter to minimum SOR values
2014-08-07 12:09:19 -04:00
683baff375
Merge pull request #697 from broadinstitute/ldg_inbreedingCoeffForMultiallelics
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Fix nullPointerException
2014-08-07 11:57:39 -04:00
f532f1f843
Fix nullPointerException
2014-08-07 10:13:17 -04:00
0b72f7a16d
Merge pull request #685 from broadinstitute/ldg_inbreedingCoeffForMultiallelics
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Update inbreeding coefficient calculation to give a better estimate for ...
2014-08-07 09:00:09 -04:00
74affcc077
Update inbreeding coefficient calculation to give a better estimate for multialleleic sites
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Add unit test for compound het and for multiallelic hets
2014-08-07 08:12:47 -04:00
b9486f5b4d
Merge pull request #693 from broadinstitute/ldg_SORfromHC
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Allow SOR to be calculated from HC
2014-08-06 21:48:09 -04:00
5f31e54d67
Merge pull request #696 from broadinstitute/pd_DoC_sorting
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Fix sample sort order bug in DepthOfCoverage
2014-08-06 08:35:35 -04:00
6fa4764fc1
Merge pull request #694 from broadinstitute/pd_check_missing_arg_values
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Improved detection of missing argument values
2014-08-06 08:32:22 -04:00
b0c026e671
Fix sample sort order bug in DepthOfCoverage
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Rare bug triggered by hash collision between sample names
PT 66183936
2014-08-05 21:55:34 -04:00
593663d9b6
Improved detection of missing argument values
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In particular, it was possible to specify arguments for Files or Compound types without values
Added a special "none" value for annotations, since a bare "-A" is no longer allowed
Delivers PT 71792842 and 59360374
2014-08-05 20:31:31 -04:00
03e7ee6e9c
Merge pull request #695 from broadinstitute/pd_genotype_concordance_doc
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Documentation fix (closed HTML tag)
2014-08-05 07:15:40 -04:00
359fe150c9
Documentation fix (closed HTML tag)
2014-08-04 23:19:16 -04:00
5533199402
Allow SOR to be calculated from HC
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Refactor StrandBiasTest classes
2014-08-01 20:47:58 -04:00
e69b0d6316
Merge pull request #692 from broadinstitute/rp_typo_analyze_covariates
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Fixing typos in AnalyzeCovariates
2014-07-31 10:39:31 -04:00
63b3f7dfd3
Fixing typos in AnalyzeCovariates
2014-07-31 10:36:18 -04:00
66ccc636b8
Merge pull request #691 from broadinstitute/ldg_update_htsjdk
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Update GATK to work with latest htsjdk
2014-07-30 14:32:23 -04:00
4373922ee6
Update GATK to work with latest htsjdk
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ValidationStringency was moved from htsjdk.samtools.SAMFileReader to htsjdk.samtools
samtools find BAM index file method was also moved (and made public!)
2014-07-30 12:05:14 -04:00
d69af637bf
Merge pull request #690 from broadinstitute/vrr_fix_non_diploid_unsupproted_message_in_haplotype_caller
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Add diploid only support message to HaplotypeCaller
2014-07-29 22:50:00 -04:00
750eb4b5a6
Add diploid only support message to HaplotypeCaller
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Story:
https://www.pivotaltracker.com/story/show/73440292
Changes:
- Just add the conditional in HaplotypeCaller#initialize
Testing:
- Nothing added, checked locally, trivial change that would eventually be removed anyway.
2014-07-29 17:05:36 -04:00
43bd6b4436
Merge pull request #689 from broadinstitute/eb_fix_samrecord_test_constructor
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The copy constructor for a GATKSAMRecord (used for testing only) should ...
2014-07-23 23:03:30 -04:00
84af1fc75f
The copy constructor for a GATKSAMRecord (used for testing only) should use the actual read's contig index, not its mate's.
2014-07-23 15:31:03 -04:00
881fc9cc35
Merge pull request #687 from broadinstitute/vrr_omniploidy_assesment_na12878
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Further changes to AssessNA12878 for evaluating Omniploidy
2014-07-22 14:45:59 -04:00
a3d180ac43
Updated na12878kb-utils with classes from old ant StingUtils.jar.
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Fixed package names post picard/htsjdk renaming.
2014-07-22 23:31:47 +08:00
8c14609477
Added -gtType argument to AssessNA12878 to stratify assessment based on true genotype call in NA12878 (or input call if the former is not in KB).
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Story:
https://www.pivotaltracker.com/story/show/75028590
Changes:
Added the possibility of indicating the genotype type to consider (with argument [-gtType TYPE]*, where TYPE is HET, HOM_REF or HOM_VAR)
Removed conditional Het evaluation based on input ploidy; now you need to use -gtType explictly.
Tests:
Added integration tests to check on new argument (-gtType) behaviour in AssessNA12878KnowledgeBaseTest
2014-07-22 11:02:36 -04:00
0798a4b768
Update pom versions to mark the start of GATK 3.3 development
2014-07-17 12:09:33 -04:00
323f22f852
Update pom versions for the 3.2 release
2014-07-17 12:06:22 -04:00
98d88eb07e
Fixed IndexOutOfBounds error associated with tail merging.
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Don't expand out source nodes for tail merging, since that's a head merging action only.
This shows up as a bug only because we now allow merging tails against non-reference paths.
2014-07-17 12:04:22 -04:00
799071b520
Merge remote-tracking branch 'unstable/master'
2014-07-14 14:07:16 -04:00
104d94a1ac
Merge pull request #686 from broadinstitute/gg_gatkdocs_updates
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Various documentation improvements
2014-07-14 12:10:36 -04:00
a6f632874b
Various documentation improvements
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- Edited intervals merging docs for correctness & clarity
- Edited VQSR arg docs and made mode required (+added -mode SNP to VQSR tests)
- Moved PaperGenotyper to Toy Walkers to declutter the actually useful docs
- Moved GenotypeGVCFs to Variant Discovery category and clarified a few points
- Clarified that the -resource argument depends on using the -V:tag format
- Clarified how the pcr indel model works
- Added caveat for -U ALLOW_N_CIGAR_READS
- Added MathJax support for displaying equations in GATKDocs
- Updated HC example commands and caveats
2014-07-14 12:03:03 -04:00
db53d096c9
Merge pull request #684 from broadinstitute/ks_add_cofoja_to_gatk_packages
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Added cofoja to the gatk packages for tests to pass.
2014-07-14 11:15:49 -04:00
2138aa135c
Merge pull request #683 from broadinstitute/eb_disable_complex_variant_merging_PT74816146
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Disable the complex variant merging for now, as requested by ATGU
2014-07-13 08:57:13 -04:00
ecefcb383d
Disable the complex variant merging for now, as requested by ATGU
2014-07-11 17:27:40 -04:00
c7e357eb59
Added cofoja to the gatk packages for tests to pass.
2014-07-11 23:19:42 +08:00
b8751ad598
Merge pull request #680 from broadinstitute/ldg_VQSRscript
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Update VQSR Rnd BQSR script generation code for compatibility with late...
2014-07-11 10:16:37 -04:00
4f4ff5c327
Merge pull request #682 from broadinstitute/ks_revert_md5_db_per_test
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Reverting md5 db per test
2014-07-11 03:42:18 +08:00
193e389b41
Merge pull request #679 from broadinstitute/eb_better_tail_merging_PT74222522
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Improved tail merging: now tails can be merged to branches that are not ...
2014-07-10 13:54:33 -04:00
598b481733
Merge pull request #671 from broadinstitute/vrr_omniploidy_assesment_na12878
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Now AssessNA12878 can handle different input ploidy for omniploidy asses...
Story:
https://www.pivotaltracker.com/story/show/74469346
2014-07-10 13:19:32 -04:00
18f6d56b4c
Revert "Using the base directory for each test run when outputting MD5DB mismatches."
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This reverts commit f192f032a153755a84b1d682f6e652a7c6787fb9.
2014-07-11 01:11:25 +08:00
cc09ef9190
Revert "Appending to md5db in the gatkdir, with additional logging."
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This reverts commit 0aa2884f7b006f5d48c325bf942b92c183e45074.
2014-07-11 01:11:20 +08:00
a105cc4c0a
Merge pull request #681 from broadinstitute/dr_md5mismatch_generator_script
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Shell script to generate md5 mismatches file from a Bamboo log of an integration test run
2014-07-10 10:40:09 -04:00
af0aab8791
Shell script to generate md5 mismatches file from a Bamboo log of an integration test run
2014-07-10 10:32:10 -04:00
1d97b4a191
Improved tail merging: now tails can be merged to branches that are not entirely reference.
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This is useful for e.g. cases where there are SNPs on insertions. Before tails were forced to be merged
(incorrectly) only to a reference node, but now they can be merged to any path in the graph from which they
directly branch.
Also, I've transferred over Ryan's code to refuse to process kmer sizes such that there are non-unique kmers
in the reference sequence with them.
2014-07-10 08:57:01 -04:00
aecd34d274
Merge pull request #677 from broadinstitute/ks_md5_db_per_test_type
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Appending to md5db in the gatkdir, with additional logging.
2014-07-10 17:53:24 +08:00
5eee065133
Merge pull request #674 from broadinstitute/rp_improve_genotyping
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Improvements to genotyping accuracy.
2014-07-09 16:03:09 -04:00
a7d1904c63
Appending to md5db in the gatkdir, with additional logging.
2014-07-10 03:58:47 +08:00
Valentin Ruano-Rubio
Ryan Poplin
Eric Banks
Tim Fennell
Laura Gauthier
Phillip Dexheimer
Khalid Shakir
David Roazen
Geraldine Van der Auwera
kshakir