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
ed7ff65b2e
Merge pull request #1169 from broadinstitute/gvda_typo_fix_#1159
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Trivial doc typo fix
2015-09-25 22:57:17 -04:00
118c559278
Trivial doc typo fix
2015-09-25 18:15:29 -04:00
c7f76b945e
addressing PR comments
2015-09-24 15:42:51 -04:00
a5f4b4305b
Revived this walker for GP; it does a simple super-fast coverage analysis with GC content and number of dbsnp variants annotated
2015-09-24 13:23:05 -04:00
0dacf60012
Changed calls for RGQ=0 from 0/0 to ./. in output of GenotypeGVCFs.
2015-09-23 15:35:09 -04:00
ac8b326b92
Merge pull request #1155 from broadinstitute/ms_fix_ignoreAllFilters
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Fix for ignoreAllFilters
2015-09-23 14:11:10 -04:00
db9aa9cda6
Fix for ignoreAllFilters
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Changed test file
Remove extra data file
2015-09-22 09:12:36 -04:00
de97c38a30
Merge pull request #1163 from broadinstitute/ami-fix-typo-ASEReadCounter
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fix typo in the ASEReadCounter document
2015-09-21 15:46:31 -04:00
1ad00cc9d4
fix typo in the ASEReadCounter document
2015-09-21 15:30:06 -04:00
b1cc48da05
Merge pull request #1158 from broadinstitute/ms_HSmetrics
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Adding PER_TARGET_COVERAGE option to CalculateHsMetrics wrapper
2015-09-18 13:38:41 -04:00
cdfe0d7b7c
Adding PER_TARGET_COVERAGE option
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Comments addressed
2015-09-18 09:34:51 -04:00
aadf6645f6
Merge pull request #1097 from broadinstitute/rhl_validatevariants_al_cutoff
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Allow overriding ValidateVariants' hard-coded cutoff for allele length
2015-09-17 14:00:59 -04:00
3ecabf7e45
Allow overriding ValidateVariants' hard-coded cutoff for allele length
2015-09-17 10:49:14 -04:00
5870225f83
Merge pull request #1153 from broadinstitute/ms_excess_het
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Excess Het P-value
2015-09-15 11:52:25 -04:00
7e894f3b4c
Merge pull request #1148 from broadinstitute/ks_cram_crai
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Using `SamIndexes.asBaiSeekableStreamOrNull()` to support `.cram.crai`.
2015-09-14 23:24:41 -04:00
24e24b9468
Using `SamIndexes.asBaiSeekableStreamOrNull()` to support `.cram.crai`.
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Updated other IntelliJ IDEA warnings in GATKBAMIndex.
Updated example .cram files to match versions generated by current GATK/HTSJDK.
Bumped HTSJDK and Picard to 1.139 releases.
Added support for using `-SNAPSHOT` of HTSJDK in the future.
2015-09-14 12:20:36 -04:00
2507bf8d17
Fixed 7-PL genotypes in InbreedingCoeff tests
2015-09-14 12:00:45 -04:00
d767e1722e
Excess Het P-value
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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
b5cda3e7dc
Merge pull request #1154 from broadinstitute/ldg_disableFargoQuery
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Disable test that checks a bam that's moved to Fargo (a.k.a. AWS)
2015-09-14 11:57:57 -04:00
89fc8f04db
Disable tests that checks a bam that's moved to Fargo (a.k.a. AWS)
2015-09-14 09:29:52 -04:00
3db0686dc4
Merge pull request #1133 from broadinstitute/ldg_fixInputPriors
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Make sure inputPriors get used everywhere if they are specified
2015-09-12 11:24:31 -04:00
53b506a0b8
Make sure inputPriors get used if they are specified
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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
5fe568c664
Merge pull request #1151 from broadinstitute/rhl_fix_snpmask
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Mask snps with --snpmask
2015-09-09 20:50:05 -04:00
83a7012d69
Mask snps with --snpmask
2015-09-09 16:20:48 -04:00
b0dea2ccca
Merge pull request #1150 from broadinstitute/eb_keep_iupac_in_IR
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Don't have the Indel Realigner change IUPAC reference bases.
2015-09-04 13:43:34 -04:00
5f76ae6a37
Don't have the Indel Realigner change IUPAC reference bases.
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This change doesn't affect the performance of the Indel Realigner at all (as per tests).
This is just a request from the Picard side (where further testing is happening).
2015-09-04 13:42:23 -04:00
cad81a6181
Merge pull request #1149 from broadinstitute/ldg_fixCGPbugForAndrea
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Fix bug when using --ignoreInputSamples
2015-09-04 11:17:15 -04:00
a8851e6763
Merge pull request #1127 from broadinstitute/rhl_hc_qd
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Compute genotype before info field annotations
2015-09-03 12:21:27 -04:00
29ac64f6ce
Calculate GenotypeAnnotations before InfoFieldAnnotations
2015-09-03 09:22:46 -04:00
4769ef8dad
Fix bug when using --ignoreInputSamples
2015-09-02 09:27:06 -04:00
4464c04c9c
Merge pull request #1135 from broadinstitute/sl_issue_1056
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Added file-extension--dependent interval-list output to RealignerTargetCreator.
2015-08-31 16:09:22 -04:00
41256e1405
Added file-extension--dependent interval-list output to RealignerTargetCreator.
2015-08-31 11:22:18 -04:00
Takuto Sato
Ron Levine
Chris Norman
ldgauthier
Eric Banks
Geraldine Van der Auwera
Kate Noblett
kshakir
Khalid Shakir
Johan Dahlberg
samuelklee
Samuel Lee
meganshand
Ami Levy Moonshine