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
c10fcae25d
Merge pull request #1109 from broadinstitute/bh_ROC_NA12878
...
Logistic transform of MQ + jitter to capped MQ in VariantDataManager
2015-08-20 11:18:10 -04:00
eae4c875a9
Logistic transform of MQ + jitter to capped MQ in VariantDataManager
2015-08-20 11:10:45 -04:00
beec624a63
Move htsjdk & picard to rev 1.138
2015-08-20 10:42:25 -04:00
cd9db60ce2
Merge pull request #1134 from broadinstitute/gvda_cgp_docfix_1131
...
Fixed missing code tag
2015-08-14 14:59:13 -04:00
5a875cb841
Fixed missing code tag
2015-08-14 14:58:28 -04:00
e89c510ac5
Merge pull request #1115 from broadinstitute/ms_wgsmetrics_wrapper
...
CollectWgsMetrics wrapper for queue
2015-08-14 10:25:31 -04:00
5c9935ba10
Adding CollectWgsMetrics wrapper for queue
...
Fix license
Fixed IncludeBQHistogram
2015-08-14 10:18:12 -04:00
69fd4af15a
Merge pull request #1111 from jsilter/overclippedreadfilter_endsoption
...
Add additional option to OverclippedReadFilter
2015-08-12 10:43:52 -04:00
62625b4bc6
Add option to not require soft-clips on both ends
...
Previous version of OverclippedReadFilter would only filter a read if both ends of a read had a soft-clipped block.
This adds a boolean option to relax that requirement, and only require 1 soft-clipped block, while also filtering on read length - softclipped length
2015-08-12 10:38:27 -04:00
d77611292f
Merge pull request #1113 from broadinstitute/ks_cram_with_index
...
Switched to using CRAM's SamReader.Indexing implementation.
2015-08-11 21:47:10 -03:00
9bee183f6c
Switched to using CRAM's SamReader.Indexing implementation.
...
CRAM now requires .bai index, just like BAM.
Test updates:
- Updated existing MD5s, as TLEN has changed.
- Tests multiple contigs.
- Tests several intervals per contig.
- Tests when `.cram.bai` is missing, even when `.cram.crai` is present.
Updated gatk docs for CRAM support, including:
- Arguments that work for both BAM and CRAM listed as such.
- Arguments that don't work for CRAM either explicitly say "BAM" or "doesn't work for CRAM".
- Instructions on how to recreate a `.cram.bai` using cramtools.
Cleaned up IntelliJ IDEA warnings regarding `Arrays.asList()` -> `Collections.singletonList()`.
2015-08-11 17:52:49 -03:00
822d6e9b5b
Merge pull request #1123 from broadinstitute/gvda_updatelicenses_1118
...
Updated licenses for 2015
2015-08-10 18:46:47 -04:00
19bbe45cbc
Updated licenses for 2015
2015-08-06 15:23:11 -04:00
9554e06952
Merge pull request #1119 from broadinstitute/db_diff_objects
...
Moved DiffObjects from test to main (issue #1116 )
2015-08-06 14:43:39 -04:00
ddb01058d3
moved DiffObjects
2015-08-05 21:19:02 -04:00
893c09b6e0
Merge pull request #1107 from broadinstitute/db_issue_1052
...
UnifiedGenotypingEngine queries VariantContext for model if not given
2015-08-05 21:16:29 -04:00
5fcc3788bd
UnifiedGenotypingEngine queries VariantContext for model if not given
2015-08-05 15:30:37 -04:00
c34d8174fc
Merge pull request #1114 from broadinstitute/eb_fix_IR_secondary_mates
...
Patch for the incorrect "fixing" of mates when supplementary alignments are present
2015-08-05 14:13:24 -04:00
df033f674d
Patch for the incorrect "fixing" of mates when supplementary alignments are present.
...
Note that this patch involves ignoring supplementary alignments. Ideally we would want
to fix their mates properly but that would require a major refactoring of this soon-to-be
deprecated tool.
2015-08-05 12:55:39 -04:00
f73871c865
Merge pull request #1098 from broadinstitute/vrr_rcm_is_active_calculateGenotypes
...
Faster implementation of the active state profile value calculation w…
2015-07-30 10:57:33 -04:00
604fb7aaf8
Faster implementation of the active state profile value calculation when running HC with a single sample.
...
Find out about a dev-bug and added TODOs (reported in #1096 ).
Addresses issue #1095 .
Conflicts:
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
2015-07-30 10:56:05 -04:00
9819624801
Merge pull request #1105 from broadinstitute/gvda_typo_fixes_1087_1042
...
Fixed typos and made some argument docs improvements
2015-07-29 23:37:00 -04:00
Laura Gauthier
Ron Levine
Eric Banks
samuelklee
Samuel Lee
kcibul
Mark Fleharty
Bertrand
Mark Fleharty
Geraldine Van der Auwera
meganshand
Yossi Farjoun
Jacob Silterra
kshakir
Khalid Shakir
David Benjamin
Valentin Ruano Rubio
vruano