44348a3761
Merge pull request #363 from broadinstitute/md_het_docs
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Better docs on the meaning of heterozygosity
2013-08-07 04:28:16 -07:00
318f7e74e4
Better docs on the meaning of heterozygosity
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-- [delivers #53522209 ]
2013-08-07 07:27:45 -04:00
dd0e6409c6
Merge pull request #367 from broadinstitute/md_hc_ref_fix
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Bugfix for ReferenceConfidenceModel
2013-08-06 20:37:08 -07:00
40bc7d6a9c
Bugfix for ReferenceConfidenceModel
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-- In the case where there's some variation to assembly and evaluate but the resulting haplotypes don't result in any called variants, the reference model would exception out with "java.lang.IllegalArgumentException: calledHaplotypes must contain the refHaplotype". Now we detect this case and emit the standard no variation output.
-- [delivers #54625060 ]
2013-08-06 16:00:32 -04:00
6dfd17122f
Merge pull request #362 from broadinstitute/rp_single_sample_hc_pipeline
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Adding single sample HC qscript for Mauricio.
2013-08-06 12:11:50 -07:00
ee0aba224c
Adding single sample HC qscript for Mauricio.
2013-08-06 15:10:15 -04:00
81a74351fd
Merge pull request #360 from broadinstitute/rp_vqsr_ordering_of_annotations_bug
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Fix for the VQSR visualization script with the new ordering of annotatio...
2013-08-03 09:49:42 -07:00
a46f633bd6
Fix for the VQSR visualization script with the new ordering of annotations.
2013-08-02 19:10:45 -04:00
af36c7ce9a
Update QScript.scala
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Relaxing addAll parameter type from Seq to Traversable to make it slightly more flexible.
2013-08-02 14:09:26 -04:00
08a7ef6620
Merge pull request #358 from broadinstitute/md_tribble_reuse_query_stream
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Rev picard to get optimized tribble feature reads
2013-08-02 10:29:39 -07:00
d5dd3b23db
Rev picard to get optimized tribble feature reads
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-- The previous version of TribbleIndexedFeatureReader.query() would open a RandomAccessFile each time the GATK crossed a shard boundary. When running with -L wex.intervals (or any time there were lots of intervals) we'd be opening and closing enormous numbers of files, radically slowing down the GATK. With these patched versions of Tribble we see something like the following performance improvements:
SelectVariants with -L wex.intervals on my local machine against non-local file
pre-patch => 3 hours
post-patch => 30 seconds
2013-08-02 10:31:36 -04:00
9316a70d1e
Merge pull request #355 from broadinstitute/eb_add_error_handling_to_kb
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Added error handling to the newly added sites iterator so that it doesn't NPE when it encounters a bad record
2013-08-02 06:40:41 -07:00
ae5fc4c726
Merge pull request #356 from broadinstitute/mc_refbias
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Reference bias walker
2013-08-02 06:30:56 -07:00
8a1e2d58ef
Merge pull request #357 from broadinstitute/mc_resort_haplotypes
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Better caching for the HaplotypeCaller (significant speed up on NA12878 chr20!!)
2013-08-02 06:29:41 -07:00
3e75262a3e
Reference bias walker
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Calculates reference bias based on the AD genotype field instead of AB. This is slightly more meaningful for indels and still a good estimator for snps.
2013-08-02 01:44:57 -04:00
285ab2ac62
Better caching for the HaplotypeCaller
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Problem
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Caching strategy is incompatible with the current sorting of the haplotypes, and is rendering the cache nearly useless.
Before the PairHMM updates, we realized that a lexicographically sorted list of haplotypes would optimize the use of the cache. This was only true until we've added the initial condition to the first row of the deletion matrix, which depends on the length of the haplotype. Because of that, every time the haplotypes differ in length, the cache has to be wiped. A lexicographic sorting of the haplotypes will put different lengths haplotypes clustered together therefore wasting *tons* of re-compute.
Solution
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Very simple. Sort the haplotypes by LENGTH and then in lexicographic order.
2013-08-02 01:27:29 -04:00
0b062e7f22
Merge pull request #354 from broadinstitute/eb_fix_rr_count_encoding
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Two reduce reads updates/fixes
2013-08-01 12:34:19 -07:00
e5be038f1a
Added error handling to the newly added sites iterator so that it doesn't NPE when it encounters a bad record.
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Added a unit test that exactly replicates the behavior.
2013-08-01 15:25:20 -04:00
1e396af4d0
Two reduce reads updates/fixes:
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1. Removing old legacy code that was capping the positional depth for reduced reads to 127.
Unfortunately this cap affectively performs biased down-sampling and throws off e.g. FS numbers.
Added end to end unit test that depth counts in RR can be higher than max byte.
Some md5s change in the RR tests because depths are now (correctly) no longer capped at 127.
2. Down-sampling in ReduceReads was not safe as it could remove het compressed consensus reads.
Refactored it so that it can only remove non-consensus reads.
2013-08-01 14:34:59 -04:00
ec3c885a25
Merge pull request #353 from broadinstitute/rp_HC_updates_for_1000G_and_WGS_calling
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Max number of haplotypes to evaluate no longer grows unbounded with the ...
2013-07-31 08:29:06 -07:00
4f3411f3d4
Max number of haplotypes to evaluate no longer grows unbounded with the number of samples. This is necessary for multi-sample calling projects with over 100 samples.
2013-07-31 10:48:55 -04:00
00cedd0bd3
Merge pull request #352 from broadinstitute/yf_SNPEFF_Stratifier
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moved SnpEffUtilUnitTest to public tree
2013-07-30 14:52:33 -07:00
284176cd7b
moved SnpEffUtilUnitTest to public tree
2013-07-30 17:51:40 -04:00
b8709b1942
Merge pull request #332 from broadinstitute/st_fpga_hmm
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FPGA support for PairHMM
2013-07-30 14:21:21 -07:00
ac06829194
Merge pull request #349 from broadinstitute/yf_SNPEFF_Stratifier
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Adding a representation of the hierarchy of flags output by snpEff (Yoss...
2013-07-30 12:42:25 -07:00
d2860a5486
Adding a representation of the hierarchy of flags output by snpEff (Yossi) and a stratifier whose output states are coding regions, genes, stop_gain, stop_lost and splice sites, all determined by the snpEff hierarchy (J. Rose)
2013-07-30 15:38:32 -04:00
7b731dd596
Removed native method call
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and fixed indentation.
2013-07-30 13:59:58 -04:00
cf46256356
Merge pull request #350 from broadinstitute/chartl_genotypeconcordance_doc_cleanup
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Add <pre> tags to the Genotype Concordance docs. Tables were not being d...
2013-07-29 16:17:26 -07:00
464a5b229d
Add <pre> tags to the Genotype Concordance docs. Tables were not being displayed properly.
2013-07-29 15:48:17 -07:00
678d038c76
Merge pull request #348 from broadinstitute/gg_gatkdoc_fixes
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Gg gatkdoc fixes
2013-07-26 13:17:51 -07:00
3063d82797
Fixed example in CallableLoci gatkdoc
2013-07-26 15:51:31 -04:00
fc4a8b1dd0
Fixed example in DoC gatkdoc
2013-07-26 15:51:30 -04:00
660b075900
Added deprecation notice for SomaticIndelDetector
2013-07-26 15:51:30 -04:00
5ad99c362d
Added caveat to gatkdocs for MAPQ read transformers & cleaned up AB annotation gatkdocs
2013-07-26 15:51:30 -04:00
0ea3f8ca58
Added function to gatkdocs to specify what VCF field an annotation goes in (INFO or FORMAT)
2013-07-26 15:51:30 -04:00
edbd17b8e0
Added note of caution to VQSR gatkdocs for option BOTH of recalibration mode
2013-07-26 15:51:29 -04:00
f52196496d
Merge pull request #347 from broadinstitute/eb_more_dnagling_tail_improvements
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More specific fix for the dangling tail edge case with a single leading deletion.
2013-07-26 07:25:47 -07:00
66db412ad0
Merge pull request #345 from broadinstitute/rp_vqsr_sort_annotations
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Automatically order the annotation dimensions in the VQSR by their stand...
2013-07-26 07:23:42 -07:00
8c205dda1b
Automatically order the annotation dimensions in the VQSR by their standard deviation instead of the order they were specified on the command line.
2013-07-26 10:22:43 -04:00
924d9b7ef4
Merge pull request #344 from lbergelson/lb_library_read_filter
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Adding LibraryReadFilter.
2013-07-26 06:44:53 -07:00
7c43b5f26a
Adding LibraryReadFilter.
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--Moving LibraryReadFilter which has been part of Mutect into gatk public.
--Added an additional check for null values.
2013-07-26 09:32:14 -04:00
9372c5ef41
Merge pull request #334 from broadinstitute/mc_generic_input_for_qualify_missing_intervals
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QualifyMissingIntervals: support different formats
2013-07-25 12:39:26 -07:00
71eb944e62
Adding CnyPairHMMUnitTest
2013-07-25 14:19:50 -05:00
1b25cf471c
Merge pull request #341 from broadinstitute/eb_make_all_rr_stranded
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Eb make all rr stranded
2013-07-25 11:50:43 -07:00
5dfa863caa
Fully stranded implementation of RR (plus bug fix for insertions and het compression).
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Now only filtered reads are unstranded. All consensus reads have strand, so that we
emit 2 consensus reads in general now: one for each strand.
This involved some refactoring of the sliding window which cleaned it up a lot.
Also included is a bug fix:
insertions downstream of a variant region weren't triggering a stop to the compression.
2013-07-25 14:48:53 -04:00
0a2b5ddadf
More specific fix for the dangling tail edge case with a single leading deletion.
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The previous fix was too general (and therefore incorrect) and caused the HC to exception out.
Added "unit" test for this exact case.
2013-07-25 12:24:46 -04:00
31ab0824b1
quick indentation fixes to FPGA code
2013-07-24 14:09:49 -04:00
e5aab22680
Merge pull request #342 from broadinstitute/eb_fix_mq_in_rbp
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Fixing ReadBackedPileup to represent mapping qualities as ints, not (signed) bytes.
2013-07-24 09:42:13 -07:00
6df43f730a
Fixing ReadBackedPileup to represent mapping qualities as ints, not (signed) bytes.
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Having them as bytes caused problems for downstream programmers who had data with high MQs.
2013-07-23 23:47:15 -04:00
71222bff45
Merge pull request #340 from broadinstitute/eb_fix_okaytomiss_arg
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Various updates for KB, mostly so that reviews through IGV work properly...
2013-07-21 19:01:01 -07:00
Mark DePristo
Eric Banks
Ryan Poplin
lbergelson
jmthibault79
Mauricio Carneiro
Yossi Farjoun
droazen
Joseph Rose
chartl
Geraldine Van der Auwera
sathibault