643516b3b2
Merge pull request #1310 from broadinstitute/rhl_doc_sample_gene_summary_header
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Fix sample_gene_summary reports header order
2016-03-09 09:12:36 -05:00
99532f40c1
Merge pull request #1312 from broadinstitute/ldg_fixASheaders
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Add AS_culprit and AS_VQSLOD to VCF header in ApplyRecalibration so o…
2016-03-09 08:46:34 -05:00
28cfb06513
Add AS_culprit and AS_VQSLOD to VCF header in ApplyRecalibration so output passes VCF validation
2016-03-09 08:22:58 -05:00
244a217ee7
Fix sample_gene_summary reports header order
2016-03-08 22:21:51 -05:00
dcc6c0f2aa
Merge pull request #1306 from broadinstitute/rhl_doc_overlapping_genes
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Output coverage for all overlapping genes in DepthOfCoverage
2016-03-08 13:28:30 -05:00
aa7a8e17df
Merge pull request #1304 from broadinstitute/ldg_fixROCCurveHomRef
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Remove homRef calls in NA12878 from true positive/false positive counts
2016-03-07 11:50:40 -05:00
7d2c56f681
Merge pull request #1299 from broadinstitute/gvda_doc_updates
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Documentation updates
2016-03-04 16:06:12 -08:00
2b70f14740
Misc documentation improvements
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Added caveat to VariantFiltration documentation
Fixed PON creation example in M2 doc
Improved MalformedReadFilter doc
Updated N CIGAR error message
2016-03-03 15:48:54 -08:00
4d203b895a
added support for overlapping exons/genes in DepthOfCoverage
2016-03-03 15:09:54 -05:00
36a2297f79
Clarify how UNKNOWN truth sites are treated
2016-03-02 17:32:39 -05:00
c1076bcc23
Reconcile ROC curve numbers with AssessNA12878:
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Exclude homRefs and no-calls, trim alleles, split het-non-refs
Add arg to include unknowns as TPs in order to match AssessNA12878
Add in check for KB sites that are monomorphic in NA12878
2016-03-02 14:02:39 -05:00
8c15d3ccd8
Merge pull request #1303 from broadinstitute/rhl_fix_test_ranksums
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Modify MD5s to correct RankSum annotations
2016-03-01 16:09:29 -05:00
e5c5804141
Modify MD5s to correct RankSum annotations
2016-03-01 14:05:51 -05:00
625941dc50
Merge pull request #1290 from broadinstitute/rhl_sac_nonref
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StrandAlleleCountsBySample selects most likely only from VCF alleles
2016-02-29 17:05:57 -05:00
5e2ffc188b
Merge pull request #1295 from broadinstitute/rhl_sv_error_output_1194
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Correct error messages and error handling in multiple tools
2016-02-29 17:05:24 -05:00
32bd02aa9d
Merge pull request #1186 from broadinstitute/ms_RankSum
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Removes Dithering from Rank Sum Test
2016-02-29 14:10:37 -05:00
40a5adf767
Change error output to use the correct argument
2016-02-29 13:21:03 -05:00
80a22aad77
StrandAlleleCountsBySample selects most likely only from VCF alleles
2016-02-29 12:41:55 -05:00
c7e0f5b225
Removes Dithering from Rank Sum Test
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Fixing empty group case
Fixing MD5s
First comments addressed
Added permutation test
Adding new RankSum to AS_RankSum
Speeding up permutation algorithm and updating MD5s
Missed a few tests
Addressing comments
Changing md5s
2016-02-29 11:45:27 -05:00
3b327ac0e4
Merge pull request #1273 from broadinstitute/yf_Fix_GATK_bug_around_hg38_contignames
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Various fixes surrounding GenomeLoc parser and hg38 contig names
2016-02-02 07:10:58 -05:00
7896055be3
- Fixed bug in GenomeLoc parser
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- Added a warning when two contigs are too similar that it might cause problems with parsing
- Added tests of modified parser and of warning.
2016-02-02 06:53:22 -05:00
8ab2eef6f0
Merge pull request #1282 from broadinstitute/ts_annotation
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Allele specific insert size ranks sum annotation
2016-01-29 18:13:46 -05:00
243a0fcb74
Allele-specific insert size ranksum annotation
2016-01-28 16:03:57 -05:00
1e4a98827c
Merge pull request #1278 from broadinstitute/gvda-expose_queue_setting
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Expose time between checks as CLI argument (Queue)
2016-01-28 11:00:36 -05:00
0e969d9c5d
Merge pull request #1279 from broadinstitute/ldg_removeExtraKBsamples
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Fix rogue false negatives from non-NA12878 samples in knowledgebase
2016-01-28 08:32:20 -05:00
633e729608
Reverted setupNA12878kb script to use old-style path names
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Import files are now derived from /humgen/gsa-hpprojects/NA12878Collection/knowledgeBase/runme.allLoci.csh, which subsets samples to NA12878 but maintains all loci
2016-01-28 08:29:36 -05:00
ab5a8f0bb0
Merge pull request #1266 from broadinstitute/ldg_VQSRforAlleles
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Add new -AS mode to run VQSR (both VariantRecalibrator and ApplyRecal…
2016-01-22 13:19:11 -05:00
5592e4ead0
Add new -AS mode to run VQSR (both VariantRecalibrator and ApplyRecalibration) in an allele-specific manner
2016-01-22 13:18:21 -05:00
a46a4a6175
Expose time between checks for whether new jobs can be submitted as a user-settable parameter on CLi. Useful when testing pipelines to make idle time shorter. Contributed by @dakl (Daniel Klevebring on GATK forum).
2016-01-22 12:13:07 -05:00
76817fe5ec
Merge pull request #1276 from broadinstitute/gvda-remove_unneeded_dependency
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Remove unneeded dependency
2016-01-21 16:51:34 -05:00
c93a611ea3
Remove unneeded dependency
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Addresses https://github.com/broadgsa/gatk/pull/15 for Guillermo
2016-01-21 16:51:01 -05:00
98eba7fb53
Merge pull request #1272 from broadinstitute/rhl_rm_variant_contig_order_check
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Remove variant contig order check
2016-01-20 09:32:10 -05:00
ed933013fe
Remove variant contig order check
2016-01-16 19:32:28 -05:00
c57c32b915
Merge pull request #1270 from broadinstitute/eb_small_genotyping_optimizations
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Small optimizations to the joint calling code.
2016-01-13 08:46:57 -05:00
ab2f541d1f
Small optimizations to the joint calling code.
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Thanks to profiling I noticed that the determineCoefficient() method was being called too often.
Because it returns a constant result in half of the invocations, its value should be cached when possible.
Also, the various calls to getLog10Likelihoods() showed up in the profiler, so I pulled those out too.
All told, it speeds up the genotyping by about 10 percent according to the profiler.
2016-01-12 21:48:20 -05:00
d1565e4e6f
Merge pull request #1261 from broadinstitute/ldg_VariantsToTableMultiallelicTypes
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Allow VariantsToTable to determine each allele's type when -SMA is used
2016-01-12 10:47:22 -05:00
593c9ddf01
Allow VariantsToTable to evaluate the type of each split variant when -F TYPE and -SMA are specified
2016-01-12 08:12:29 -05:00
7f7ba446c0
Merge pull request #1269 from broadinstitute/dr_repair_3.5_tag
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Repair the 3.5 tag in unstable
2016-01-08 16:06:33 -05:00
dc5c08f940
Repair 3.5 tag in unstable by merging the missing 3.5 commit from stable
2016-01-08 15:33:15 -05:00
d9e0b7ba58
Merge pull request #1268 from broadinstitute/ldg_fixQueueTests3
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Remove "mem_free" from resident memory request params for Queue becau…
2016-01-08 12:58:46 -05:00
204cad3646
Remove "mem_free" from resident memory request params for Queue because it doesn't work and wouldn't actually reserve memory anyway
2016-01-08 10:27:56 -05:00
f002acebdf
Merge pull request #1264 from broadinstitute/rhl_max_nocall_1262
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Backport maxNoCall functionality from GATK4
2016-01-06 14:54:24 -05:00
d16ed98c9e
Backport maxNoCall functionality from GATK4
2016-01-06 11:09:38 -05:00
1d72ab099c
Merge pull request #1247 from broadinstitute/ldg_VQSRmodelOutput
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Add optional argument for VQSR to output the model to a file as a GAT…
2016-01-05 08:35:18 -05:00
37746e40f4
Merge pull request #1263 from broadinstitute/rhl_rbp_not_merging_snps
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Merge consecutive SNPs on the same read
2016-01-04 15:37:04 -05:00
fa1d90d236
Merge consecutive SNPs on the same read
2016-01-04 13:48:59 -05:00
2ddc48914e
Add optional argument for VQSR to output the model to a file as a GATKReport
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GATKReport output also has mean and variance for annotation normalization info
2016-01-04 08:37:08 -05:00
71c6709765
Merge pull request #1145 from broadinstitute/ldg_M2_HapMapSensitivity
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Fix no-normal bug; add HapMap sensitivity benchmarking
2016-01-04 08:27:37 -05:00
4b3b5636c6
Merge pull request #1265 from broadinstitute/rhl_hc_stdout_1259
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Fix exception when writing gVCF to stdout
2015-12-29 23:07:53 -05:00
aa5e88a393
Fix exception when writing gVCF to stdout
2015-12-29 15:30:53 -05:00
Geraldine Van der Auwera
ldgauthier
Ron Levine
seru71
meganshand
Yossi Farjoun
Yossi Farjoun
Takuto Sato
Eric Banks
David Roazen