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
687d2d0244
Merge pull request #1144 from broadinstitute/ldg_fixQueueTestsAgain
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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
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Little changes to M2 code and docs
2015-08-28 10:25:23 -04:00
3dc68732fb
Little changes to M2 code and docs
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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
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-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
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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
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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
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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
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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
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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
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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
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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
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CollectWgsMetrics wrapper for queue
2015-08-14 10:25:31 -04:00
5c9935ba10
Adding CollectWgsMetrics wrapper for queue
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Fix license
Fixed IncludeBQHistogram
2015-08-14 10:18:12 -04:00
69fd4af15a
Merge pull request #1111 from jsilter/overclippedreadfilter_endsoption
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Add additional option to OverclippedReadFilter
2015-08-12 10:43:52 -04:00
62625b4bc6
Add option to not require soft-clips on both ends
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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
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Switched to using CRAM's SamReader.Indexing implementation.
2015-08-11 21:47:10 -03:00
Eric Banks
Ami Levy Moonshine
meganshand
Ron Levine
ldgauthier
kshakir
Khalid Shakir
samuelklee
Samuel Lee
kcibul
Mark Fleharty
Bertrand
Mark Fleharty
Geraldine Van der Auwera
Yossi Farjoun
Jacob Silterra