b045f2d4aa
ParallelShell added as a new JobRunner
...
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
...
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
...
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
...
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
...
Fix for ignoreAllFilters
2015-09-23 14:11:10 -04:00
db9aa9cda6
Fix for ignoreAllFilters
...
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
...
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
...
Adding PER_TARGET_COVERAGE option to CalculateHsMetrics wrapper
2015-09-18 13:38:41 -04:00
cdfe0d7b7c
Adding PER_TARGET_COVERAGE option
...
Comments addressed
2015-09-18 09:34:51 -04:00
aadf6645f6
Merge pull request #1097 from broadinstitute/rhl_validatevariants_al_cutoff
...
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
...
Excess Het P-value
2015-09-15 11:52:25 -04:00
7e894f3b4c
Merge pull request #1148 from broadinstitute/ks_cram_crai
...
Using `SamIndexes.asBaiSeekableStreamOrNull()` to support `.cram.crai`.
2015-09-14 23:24:41 -04:00
24e24b9468
Using `SamIndexes.asBaiSeekableStreamOrNull()` to support `.cram.crai`.
...
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
...
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
...
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
...
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
...
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
...
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
...
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.
...
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
...
Fix bug when using --ignoreInputSamples
2015-09-04 11:17:15 -04:00
a8851e6763
Merge pull request #1127 from broadinstitute/rhl_hc_qd
...
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
...
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
687d2d0244
Merge pull request #1144 from broadinstitute/ldg_fixQueueTestsAgain
...
Update md5s for BAM header version change in Queue test output
2015-08-28 16:32:45 -04:00
a86f3909ca
Update md5s for BAM header version change in Queue test output
2015-08-28 14:19:25 -04:00
13c5a74cc7
Merge pull request #1051 from broadinstitute/ldg_M2_additionalFeatures
...
Little changes to M2 code and docs
2015-08-28 10:25:23 -04:00
3dc68732fb
Little changes to M2 code and docs
...
Make MQ threshold a parameter (compare to M1 by setting to zero)
Add logic for multiple alternate alleles in tumor
Exclude MQ0 normal reads from normal LOD calculation
Fix path errors in Dream_Evaluations.md
Move M2 eval scripts out of walkers package so they run
2015-08-27 15:31:27 -04:00
2ac5051767
Merge pull request #1063 from broadinstitute/mf_BinnedBQSR
...
-FQQ option added to BQSR to allow for fixed bins.
2015-08-25 10:17:58 -04:00
be22884138
Merge pull request #1125 from broadinstitute/bh_ROCCurveNA12878_plots
...
Bh roc curve na12878 plots
2015-08-24 15:33:56 -04:00
5a1dda8b5c
Added plots to ROCCurveNA12878 output
2015-08-24 15:31:00 -04:00
daeb55429e
Adding Static Binning to BQSR
2015-08-24 13:36:17 -04:00
4c35c2676b
Merge pull request #1036 from broadinstitute/rhl_subset_sac
...
Make GenotypeGVCFs subset Strand Allele Counts intelligently
2015-08-22 10:07:49 -04:00
2afe3f7a21
Make GenotypeGVCFs subset Strand Allele Counts intelligently
2015-08-22 08:33:09 -04:00
3b4760fb64
Merge pull request #1141 from broadinstitute/bh_fix_again_license
...
Re-ran the updateAllLicenses.sh script
2015-08-21 11:35:17 -04:00
158477ea6c
Re-ran the updateAllLicenses.sh script
2015-08-21 11:32:51 -04:00
3f5a5c0a11
Merge pull request #1140 from broadinstitute/bh_ROC_NA12878
...
Logit transform to MQ + jitter MQ capped improves VQSR
2015-08-20 18:01:46 -04:00
f61529d254
Logit transform to MQ + jitter MQ capped improves VQSR
2015-08-20 17:53:01 -04:00
900fe3f675
Merge pull request #1132 from broadinstitute/rhl_rev_htsjdk
...
Move htsjdk & picard to rev 1.138
2015-08-20 11:58:41 -04:00
Johan Dahlberg
samuelklee
Geraldine Van der Auwera
Samuel Lee
ldgauthier
meganshand
Eric Banks
Ami Levy Moonshine
Ron Levine
kshakir
Khalid Shakir
kcibul
Mark Fleharty
Bertrand
Mark Fleharty