a079d8d0d1
Breaking the utility to write @PG tags for SAMFileWriters and StingSAMFileWriters
2012-11-14 10:33:22 -05:00
dba31018f4
Implementation of BySampleSAMFileWriter
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ReduceReads now works with the n-way-out capability, splitting by sample.
DEV-27 #resolve #time 3m
2012-11-14 10:33:22 -05:00
8503db6e87
moving cancer pipeline qscript over to cmi-cancer
2012-11-14 10:33:21 -05:00
de53c32361
moving to cmi-cancer
2012-11-14 10:33:21 -05:00
ff63c53961
Increase bwa mem limit by 1 Gb - see if we can avoid random job failures that way
2012-11-14 10:33:21 -05:00
a17cd54b68
Co-Reduction implementation in ReduceReads
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ReduceReads now co-reduces bams if they're passed in toghether with multiple -I. Co-reduction forces every variant region in one sample to be a variant region in all samples.
Also:
* Added integrationtest for co-reduction
* Fixed bug with new no-recalculation implementation of the marksites object where the last object wasn't being removed after finalizing a variant region (updated MD5's accordingly)
DEV-200 #resolve #time 8m
2012-11-14 10:33:21 -05:00
f4511c0d6f
made parameters not required, fixed some null file names
2012-11-14 10:33:21 -05:00
1bfe73397f
made parameters not required, switched date sequenced format, bug fixes in pulling remote files
2012-11-14 10:33:21 -05:00
f9cc68ce17
pull metadata from metadata service
2012-11-14 10:33:20 -05:00
6d59dd3455
Scala classes were only returning direct subclasses (confirmed when inspected in debugger) so changed PluginManager to allow specifying the explicit subclass.
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Removed some generics from PluginManager for now until able to figure out syntax for requesting explicit subclass.
QStatusMessenger uses a slightly more primitive Map[String, Seq[RemoteFile]] instead of Map[ArgumentSource, Seq[RemoteFile]].
Added an QCommandPlugin.initScript utility method for handling specialized script types.
2012-11-14 10:33:20 -05:00
c0db3fe8f8
Merge branch 'develop'
2012-11-02 06:58:42 -04:00
52c635b551
Merge branch 'master' of github.com:broadinstitute/cmi-gatk
2012-11-02 06:58:21 -04:00
e03c9269ad
Damned if I do damned if I don't: SGE doesn't like more than 1 thread and BQSR scatter-gather is broken, so disable for now. Pipeline will still take forever for now
2012-11-01 15:57:45 -04:00
b9d796f502
More memory/parallelization tweaks: BQSR scatter-gather broken in latest GATK, so disabled. Used multithreading with bigger memory instead
2012-11-01 12:55:00 -04:00
2db2747723
More tweaks in pipeline parameters
2012-10-31 21:32:19 -04:00
9a1667f31b
Tweaks in SGE usage
2012-10-31 20:01:33 -04:00
6aec172c16
Merge branch 'develop' of github.com:broadinstitute/cmi-gatk into develop
2012-10-31 19:51:53 -04:00
74e842ca95
Merge branch 'develop' of https://github.com/broadinstitute/cmi-gatk into develop
2012-10-31 19:48:52 -04:00
651b1dbb97
Merge branch 'unstable' into develop
2012-10-31 12:06:09 -04:00
3dd290b142
Merge branch 'develop' of github.com:broadinstitute/cmi-gatk into develop
2012-10-31 12:00:05 -04:00
f5697532d6
Added mvninstall.queue.all target which includes private, along with supporting sub-targets.
2012-10-31 11:49:50 -04:00
7dc0e26549
Merge remote-tracking branch 'unstable/master' into unstable
2012-10-31 11:47:51 -04:00
51a9ce28e1
Merge remote-tracking branch 'unstable/master' into develop
2012-10-31 10:29:48 -04:00
55ffbec000
Fixes to set output QC files, prepare for GridEngine usage
2012-10-31 07:55:04 -04:00
eccb76c304
Only run UG in the bundle for chr20
2012-10-30 15:09:46 -04:00
e1e480a0b9
Bug fix: don't add no-call alleles to the list of ALT alleles being validated.
2012-10-30 14:54:29 -04:00
2aa28abe0a
Fixing md5s to reflect the new HapMap file
2012-10-30 14:27:10 -04:00
a3ba3e0a61
fixed invocation of indel single sample VCF filter to supply GATK classpath
2012-10-30 11:14:08 -04:00
8a402024c2
Updating bundle script to handle new naming convention of CEU trio best practices callset
2012-10-30 09:11:56 -04:00
c95e893920
Better error message for unused ALT alleles
2012-10-29 21:51:35 -04:00
b6a1967f12
Better documentation for ValidateVariants so that people realize it's used for strict validation of the VCF file. Added an option to turn off strict validation and an integration test to cover it.
2012-10-29 21:47:09 -04:00
21fa5f70ca
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-10-29 18:53:41 -04:00
5ee2feb2a3
updating pipeline test md5s
2012-10-29 18:53:27 -04:00
be902375ac
'Bug' fix: fix the error message from the vcf validator so people realize that the file fails strict validation but still adheres to the spec.
2012-10-29 16:29:27 -04:00
4e661847b2
DelocalizedBaseRecalibrator becomes the BaseRecalibrator.
2012-10-29 12:53:39 -04:00
cb7fe3f881
implementation of
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DEV-15 #resolve #time 1m
DEV-16 #resolve #time 3m
DEV-17 #resolve #time 1m
DEV-18 #resolve #time 3m
2012-10-29 12:00:36 -04:00
ac99437eec
Bug fixes to hapmap conversion in VariantsToVCF
2012-10-29 01:45:33 -04:00
43f7e8dc47
Queue installed in aws refuses to see new GATK extension, so disable for now. Reenable QC now that Rscript is installed in cloud
2012-10-28 15:58:36 -04:00
9fe79ec74b
Reenable parallelization in BQSR
2012-10-27 19:56:46 -04:00
c21bc5ac4c
Hook up duplicate metrics to script outputs. Disable GC and multiple metrics until R is installed in nodes
2012-10-27 19:48:48 -04:00
43625f652e
Shoot, mixed up the md5s last time.
2012-10-27 19:43:46 -04:00
468640476f
Merge remote-tracking branch 'unstable/master' into develop
2012-10-27 13:50:03 -04:00
f3ac5d404d
updating vcf header attribute descriptions in order to reflect correctly what's actually being written...
2012-10-26 23:52:21 -04:00
b4fbf6280a
fixing missing sample genotype bug, missing AD/DP bug, and putting annotations in more natural order (Ref/Alt)
2012-10-26 23:48:40 -04:00
ac5e58a265
Bugfix for GSA-540 / Update metadata maps when adding lines to VCFHeader
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-- https://jira.broadinstitute.org/browse/GSA-540
-- http://gatkforums.broadinstitute.org/discussion/1433/possible-bug-and-fix-in-java-code-of-vcfheader-org-broadinstitute-sting-utils-codecs-vcf-vcfheader
2012-10-26 16:34:16 -04:00
fa9b2a91d0
Bugfix for GSA-552
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-- https://jira.broadinstitute.org/browse/GSA-552
-- User reports a null exception while using VariantsToVCF:
http://gatkforums.broadinstitute.org/discussion/1461/nullpointerexception-converting-vcf3-to-vcf-using-variantstovcf
The problem is that he left out an input VCF file for the --variant argument and the command-line argument parsing code didn't catch this, so we NPE out later on.
2012-10-26 16:34:16 -04:00
682a72faf7
Hmm, thought I got all the md5s last time. Apparently not.
2012-10-26 16:10:12 -04:00
b0dcc2c78e
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-10-26 15:14:41 -04:00
610e003b93
Fixing a bug in the BQSR where the reference context gets out of sync after a read is adapter clipped inside the walker.
2012-10-26 15:14:27 -04:00
35483a7eef
Update MD5s for PrintReads with BQSR Integration Test
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The MD5s for these tests were changed in commit 87435f1074615b2cd016f042980109fd53962c8d
to match the output of a broken version of BaseRecalibration. With the patch in
commit c397102ecc1fd1d2cd8f209a8f358ab4a60b50a7, the output once again matches the
*original* MD5s for these tests, and does not vary as you increase -nct.
Final resolution to GSA-632
2012-10-26 14:25:25 -04:00
Mauricio Carneiro
Kristian Cibulskis
Guillermo del Angel
Douglas Voet
Scott Frazer
kshakir
Eric Banks
Ryan Poplin
Andrey Sivachenko
Mark DePristo
David Roazen