3de98263f5
Copy Program Records (PG) from input BAM
2017-06-01 16:01:20 -04:00
505383e504
Remove obsolete unmapped reads test for FindCoveredIntervals ( #1580 )
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Remove obsolete unmapped reads test for FindCoveredIntervals
2017-05-02 08:50:12 -04:00
a950d0778f
Add the Intel GKL as a dependency, and turn on the Intel inflater/deflater by default
2017-04-05 12:45:26 -04:00
ab75b08ea7
Remove unused compressed_block_size and close BlockCompressedInputStream
2017-02-17 12:22:53 -05:00
1d36d9fd69
Move htsjdk to ver 2.9.0 and picard to ver 2.8.3
2017-02-17 07:03:03 -05:00
e86da63d04
Update pom versions to mark the start of GATK 3.8 development
2016-12-12 08:53:23 -05:00
56f2c1ac75
Update pom versions for the 3.7 release
2016-12-12 08:49:43 -05:00
172db666d6
Output files with the vcf.gz extension are gzipped, containing .bcf not as an extension result in VCF"
2016-12-05 22:25:59 -05:00
234ccdf0c3
Merge pull request #1496 from broadinstitute/db_m2_downsampling
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Expose downsampling parameters as CLI arguments to Mutect2
2016-12-05 21:53:25 -05:00
b1f2301dd3
Add downsampling arguments to Mutect
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- maxReadsInRegionPErSample, minReadsPerAlignment start are now M2 args
- maxReadsInMemoryPerSample is an activeRegionWalker arg
2016-12-05 14:12:22 -05:00
b42dc1624b
Documentation fixes
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- Fix missing closing code block tag
- SOR fix + minor fix to template
- Minor typo fixes
- Make no_cmdline_in_header arg visible in docs
- Caveats for UG-only args that are difficult to move out of common collection
- Reference -L and -XL in -gvcf documentation
- Annotation doc fixes (dsde-docs#1289)
- Unhide some ContEst args and make Advanced
- Fix inputPrior error message
- Update web urls
- Add JEXL doc link
2016-12-05 14:09:44 -05:00
68b6f8f638
Replace VariantContextWriterFactory with VariantContextWriterBuilder
2016-11-30 16:04:25 -05:00
cfd3ffa2c0
Replace SAMFileReader with calls to SamReaderFactory
2016-10-14 11:22:54 -04:00
f6c18a5182
Throw an exception if the BQSR input covariants file is not found
2016-08-11 12:46:14 -04:00
a465c87ff8
Added support for directly reading SRA runs
2016-08-02 15:21:14 -04:00
aace73e884
Enable control of reporting periodicity
2016-07-13 07:24:03 -04:00
3c5eac8c17
Move htsjdk and picard to version 2.5.0
2016-06-28 09:42:32 -04:00
6fe80d53d0
Improve documentation
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Clarified that this also filters supplementary alignments.
2016-06-23 16:20:00 -04:00
76bb8fd9e5
Allows GatherBqsrReports to accept a .list file as input.
2016-06-22 12:39:18 -04:00
85dce75f3f
Update pom versions to mark the start of GATK 3.7 development
2016-06-01 17:21:48 -04:00
f185a75e1c
Update pom versions for the 3.6 release
2016-06-01 17:08:17 -04:00
d87345cd1d
GATKDocs overhaul
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- Fixed displaying of default values
- Removed code cruft
- Reorganized tooldoc categories and improved names
- Reorganized tools within categories where applicable
- Touched up various tool docs
- Switched default gatkdocs output to html
- Added parameter in agrregator pom to control output type
- Set gatkdocs publishing script to output php
- Deprecated GenotypeAndValidate walker
- Added back PhoneHome arguments with @Deprecated annotations
2016-05-29 16:35:08 -04:00
0769c8ae3e
Remove Phone Home
2016-05-27 16:16:29 -04:00
5b80c92cb7
Improved article linking in error messages
2016-05-27 13:49:31 -04:00
3b7e0c56bf
Moved post-IR MQ reverter filter to public
2016-05-27 12:39:58 -04:00
35a06879f1
Move htsjdk and picard to version 2.3.0
2016-05-16 14:50:00 -04:00
14fe8b1e0e
Moved BQSRGatherer and dependencies to the public module
2016-04-27 07:15:28 -04:00
f337b45724
Move htsjdk and picard to version 2.0.0
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Conflicts:
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
2016-04-25 14:51:25 -04:00
b471884d97
Added run-time information to log output
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Also updated copyright date
2016-03-11 16:43:03 -05:00
9a306ca221
Update licenses
2016-03-05 01:09:43 -08:00
2b70f14740
Misc documentation improvements
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Added caveat to VariantFiltration documentation
Fixed PON creation example in M2 doc
Improved MalformedReadFilter doc
Updated N CIGAR error message
2016-03-03 15:48:54 -08:00
ed933013fe
Remove variant contig order check
2016-01-16 19:32:28 -05:00
4767a83d8a
Update pom versions to mark the start of GATK 3.6 development
2015-11-25 01:52:51 -05:00
2570cab24c
Assorted documentation fixes, enhancements and reorganization.
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See issues referenced by the pull request for details.
2015-11-20 22:44:46 -05:00
0b3b09e3ff
Move htsjdk & picard to version 1.141
2015-11-20 16:26:26 -05:00
ccaddefa19
Validate VCF with sequence dictionary
2015-11-20 09:23:24 -05:00
19af5724c5
Fixed an NA12878 Knowledgebase test, and made the RDQ option for BQSR binning hidden
2015-10-27 09:44:26 -04:00
e776502c49
Fix Sample mergeValues failure when merging identical string values ( #1156 ).
2015-10-12 09:56:05 -04:00
3ecabf7e45
Allow overriding ValidateVariants' hard-coded cutoff for allele length
2015-09-17 10:49:14 -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
daeb55429e
Adding Static Binning to BQSR
2015-08-24 13:36:17 -04:00
beec624a63
Move htsjdk & picard to rev 1.138
2015-08-20 10:42:25 -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
9bee183f6c
Switched to using CRAM's SamReader.Indexing implementation.
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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
19bbe45cbc
Updated licenses for 2015
2015-08-06 15:23:11 -04:00
719bb15340
Merge pull request #1019 from broadinstitute/rhl_var_index_param_gz
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Indexing parameters not required if output file has the g.vcf.gz exte…
2015-06-17 14:30:20 -04:00
b35085ca28
Indexing parameters not required if output file has the g.vcf.gz extensionv
2015-06-13 11:46:56 -04:00
dbed660183
Add spannning deletions allele
2015-06-12 16:43:06 -04:00
8c81e7df95
Added a new filter that can be used to remove reads that are too small and overly clipped.
2015-05-22 14:33:35 -04:00
Ron Levine
David Roazen
Geraldine Van der Auwera
David Benjamin
Andrii Nikitiuk
sooheelee
Samuel Lee
Yossi Farjoun
meganshand
Mark Fleharty
Chris Norman
Khalid Shakir
Jacob Silterra
Eric Banks