1443ee8c7f
Fixes testPRWithConflictingArguments_qqAndSQQ to use -ql rather than -q1
2015-11-20 11:23:02 -05:00
29e86a0d01
Merge pull request #1222 from broadinstitute/yf_percent_informative_read
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Adding fraction informative reads annotation.
2015-11-18 10:08:50 -05:00
4da0d1300c
adding fraction informative reads annotation.
2015-11-18 08:39:47 -05:00
2bffe0b428
Merge pull request #1219 from broadinstitute/dr_move_GatherBqsrReports_to_protected
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Move GatherBqsrReports from private to protected
2015-11-16 22:26:54 -05:00
9d5be24778
Move GatherBqsrReports from private to protected
2015-11-10 17:40:58 -05:00
2b591d0b6f
Merge pull request #1198 from broadinstitute/ldg_moreASannotations
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Allele-specific QD and InbreedingCoeff
2015-11-10 00:35:15 -05:00
25b8ba45f4
More allele-specific annotations: AS_QD and AS_InbreedingCoeff
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Grouped default output annotations to keep them from getting dropped when -A is specified; addresses #918
Also refactored code shared by ExcessHet and InbreedingCoeff
2015-11-09 16:38:31 -05:00
fa6c1c933b
Merge pull request #1193 from broadinstitute/vrr_general_independent_af_calculator
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Added the AF independent calculator for any ploidy but seems that is no…
2015-11-07 22:14:23 -05:00
e3d5d96076
Added the AF indepdent calculator for any ploidy but seems that is not doing a good job for haploid
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Addresses issue #1078 by implementing a any-ploidy version of the independent-allele-exact-ac-calculator already available for diploids.
Notice that this will change result somewhat when dealing with noisy data (low GQs).
2015-11-07 16:17:30 -05:00
49fa06865c
Merge pull request #1207 from broadinstitute/mf_SV_bugfix
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Resolves issue #1061 to use testid1 rather than testid in two integra…
2015-11-06 08:52:38 -05:00
8857bc9b3f
Resolves issue #1061 to use testid1 rather than testid in two integrationtests.
2015-11-05 22:20:20 -05:00
975f8a8502
Merge pull request #1206 from broadinstitute/eb_suppress_alt_allele_warnings
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Suppress emission of the scary warning message from genotyping to no …
2015-11-05 16:12:50 -05:00
2cc7de4886
Suppress emission of the scary warning message from genotyping to no more than once in
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anything but DEBUG logging mode. Otherwise it fills up our output logs.
2015-11-05 14:19:21 -05:00
448b575701
Merge pull request #1204 from broadinstitute/ms_fix_SelectVariants
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Fix for out of date VCF version output from SelectVariants
2015-11-05 08:07:48 -05:00
e4627ed5c3
Addressing comments
2015-11-04 11:00:01 -05:00
b5165b8d30
Fix for out of date VCF version output
2015-11-03 17:35:47 -05:00
3d1dc303b3
Merge pull request #1197 from broadinstitute/ts_ve_nullPointer
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Prevent null pointer exception in PrintMissingComp module
2015-11-02 14:42:50 -05:00
33462c7b50
Removed the line that caused a null pointer, as the information it logged was not useful. Updated docs and added an integration test to ensure the code no longer throws the exception.
2015-11-02 12:45:09 -05:00
54ab65a340
Merge pull request #1187 from broadinstitute/ldg_variantEval_famStrat
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Enable family-level stratification (if a ped file is provided)
2015-10-30 08:00:30 -04:00
f7eb5d3082
Enable family-level stratification (if a ped file is provided)
2015-10-28 09:55:04 -04:00
4fbcfc2e36
Merge pull request #1173 from broadinstitute/ldg_AS_annotations
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New map-combine-finalize annotation framework
2015-10-27 12:04:56 -04:00
84006a629b
Merge pull request #1190 from broadinstitute/mf_makeRDQHidden
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Fixed an NA12878 Knowledgebase test, and made the RDQ option for BQSR…
2015-10-27 11:59:35 -04:00
68a2f1243d
Finished draft of code for new map-combine-reduce annotation framework
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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
19af5724c5
Fixed an NA12878 Knowledgebase test, and made the RDQ option for BQSR binning hidden
2015-10-27 09:44:26 -04:00
fcaf37279c
Finished draft of code for new map-combine-reduce annotation framework
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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
ab247e7570
Merge pull request #1189 from broadinstitute/rhl_laatv_long_allele_choke
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Allow LeftAlignAndTrimVariants to handle alleles longer than the default processing window
2015-10-26 11:02:55 -04:00
36ca9fe898
Allow LeftAlignAndTrimVariants to handle alleles longer than the default processing window
2015-10-25 20:33:56 -04:00
0d936b28c4
Merge pull request #1178 from broadinstitute/ms_ROCCurve
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ROCCurve High Confidence Mode
2015-10-22 09:19:13 -04:00
aa3087c0d1
Merge pull request #1182 from broadinstitute/rhl_laatv_multiallelic
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Update doc for multiallelics, trimming is the default behavior
2015-10-22 08:04:34 -04:00
795fe75886
Update doc for multiallelics, trimming is the default behavior
2015-10-22 04:04:09 -04:00
a57500b2fc
ROCCurve High Confidence Mode
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Integration Tests
Updated test
Changed method
Minor changes
Changed whitespace
Fixed uncalled counts and 0 in R
Fixed ReadBackedPileUp
Removed imports and changed MD5
Fixed failing test
Adding vqslod color
Updating script to create KB
Fixing integration test now that the KB is bigger
Adressing comments
2015-10-21 21:30:54 -04:00
7b067c13bd
Merge pull request #1176 from broadinstitute/ts_annotateFilterStatus
2015-10-14 16:17:49 -04:00
df7a482335
VariantAnnotator now supports annotating FILTER field from an external resource.
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Updated the docs.
2015-10-14 14:26:21 -04:00
25e0956ebb
Merge pull request #1157 from broadinstitute/cn_sample_fix
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Fix Sample mergeValues failure when merging identical string values
2015-10-12 13:19:04 -04:00
e776502c49
Fix Sample mergeValues failure when merging identical string values ( #1156 ).
2015-10-12 09:56:05 -04:00
9e168ede3e
Merge pull request #1161 from broadinstitute/rhl_va_allele_match
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VariantAnnotator checks alleles when annotating with external resource
2015-10-08 22:16:01 -04:00
2bcded11cb
VariantAnnotator checks alleles when annotationg with external resource
2015-10-08 17:01:30 -04:00
83e205c27d
Merge pull request #1177 from broadinstitute/rhl_rev_1.140
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Move htsjdk & picard to version 1.140
2015-10-08 15:17:59 -04:00
033115eae0
Move htsjdk & picard to version 1.140
2015-10-08 10:42:05 -04:00
173a34a450
Merge pull request #1174 from broadinstitute/eb_fix_combine_for_spanning_dels
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Fix for combining records in which one has a spanning deletion and ne…
2015-10-02 18:02:42 -04:00
622ec352bb
Fix for combining records in which one has a spanning deletion and needs a padded reference allele.
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This was erroring out and not working.
2015-10-02 16:28:16 -04:00
071dbf29dd
Merge pull request #1168 from broadinstitute/knoblett
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Implemented MetricsCollection evaluation module
2015-10-01 14:14:07 -04:00
506958a0b7
Implemented a new VariantEval evaulation module, MetricsCollection. Fixed null pointer exception, updated tests.
2015-09-30 17:21:30 -04:00
e9724ebac7
Merge pull request #1167 from broadinstitute/rhl_bcbs
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Implement BaseCounts per-sample
2015-09-30 10:30:30 -04:00
792142ec50
Implement BaseCounts per-sample
2015-09-30 08:59:11 -04:00
a762dcb6cf
Merge pull request #1172 from broadinstitute/ks_jd_parallel_shell
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ParallelShell added as a new JobRunner
2015-09-29 20:29:41 -03:00
384a09e991
Minor updates to previous ParallelShell commit.
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Changed `--maximumNumberOfJobsToRunConcurrently`/`-maxConcurrentRun` to `Option[Int]`.
Updated licenses.
Added basic tests.
Removed some IntelliJ warnings.
2015-09-29 09:36:37 -03:00
b045f2d4aa
ParallelShell added as a new JobRunner
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The ParallelShell job runner will run jobs locally on one node concurrently as specified by the DAG, with the option to limit the maximum number of concurrently running jobs using the flag `maximumNumberOfJobsToRunConcurrently`.
Signed-off-by: Khalid Shakir <kshakir@broadinstitute.org>
2015-09-29 09:36:37 -03:00
302a69d685
Merge pull request #1165 from broadinstitute/sl_fix_no_calls
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Changed calls for RGQ=0 from 0/0 to ./. in output of GenotypeGVCFs.
2015-09-28 12:26:18 -04:00
984b1443e8
Merge pull request #1164 from broadinstitute/gg_IntervalCovWithGC_script_1160
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Simple coverage analysis with GC content annotated
2015-09-25 23:00:21 -04:00
Mark Fleharty
Yossi Farjoun
Yossi Farjoun
Eric Banks
David Roazen
ldgauthier
Valentin Ruano Rubio
vruano
Mark Fleharty
meganshand
Takuto Sato
Ron Levine
Chris Norman
Geraldine Van der Auwera
Kate Noblett
kshakir
Khalid Shakir
Johan Dahlberg
samuelklee