9bdf36bb69
Refactoring to enable object-oriented version of haplotype calculation
2011-07-15 17:48:42 -04:00
72f4cf9c0e
Walker to perform deterministic annotation of phasing by transmission (to be compatible with RBP's definition of consecutive pairwise phasing)
2011-07-15 17:44:31 -04:00
93ec4763ee
Adding hard filters and making it the default test mode of the ReducedBAM evaluation script
2011-07-15 17:34:33 -04:00
af6c4e30c7
Deleting some useless Queue scripts
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Restoring two useful scripts to private repository:
manySampleUGPerformance.scala [calculates performance of UG and other tools as a function of the number of samples]
PostCallingQC.scala [VariantEval of a call set + R scripts to create pretty pictures. For the pipeline team to eventually own]
2011-07-15 16:51:05 -04:00
891c5d84d9
Changed ReducedReads Quality to # greater than Quality Equivalent (argument added but not yet implemented)
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Changed ReducedBAMEvaluation ot accomodate all three parameters (consolidated CallingInterval)
2011-07-15 16:36:25 -04:00
3193a3a992
Moving the PostCallingQC script to archive.
2011-07-15 16:25:01 -04:00
aa30f416a3
Resolving conflicts
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Conflicts:
private/scala/qscript/depristo/ExomePostQCEval.scala
private/scala/qscript/depristo/PostCallingQC.scala
private/scala/qscript/org/broadinstitute/sting/queue/qscripts/archive/ExomePostQCEval.scala
2011-07-15 16:21:42 -04:00
210368c128
new annotations package for menachem's script.
2011-07-15 16:11:46 -04:00
44dedf3912
moving khalid's oneoff scripts.
2011-07-15 16:08:38 -04:00
a40de4d123
No more packages with user names.
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All STABLE/PRIVATE (oneoffs) scripts that didn't get moved by their authors were put in :
org/broadinstitute/sting/queue/qscripts/archive
if you find any of these scripts that are dear to you, please move it to the appropriate package within qscripts, or create a new package that best describes what your script does.
2011-07-15 16:07:41 -04:00
e017e2bacd
Moving the mendelian violation (perhaps more than one-off) script to the appropriate package.
2011-07-15 15:51:06 -04:00
b745405195
Moving downsampling script to the calling package.
2011-07-15 15:44:25 -04:00
32a5e60e54
Removing MY old oneoff scripts.
2011-07-15 15:40:16 -04:00
9d5b560013
1. moving everyone's oneoff scala script to the appropriate package.
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2. updating pipeline tests to the new directories
2011-07-15 15:38:25 -04:00
224d373997
No need to double overload the file constructor
2011-07-15 15:19:10 -04:00
633b764877
Fixed pipeline tests accordingly.
2011-07-15 14:58:29 -04:00
63262c1440
Moving the pipeline queue scripts into a new 'pipeline' package in the org.broadinstitute.sting.queue.qscripts structure.
2011-07-15 14:56:23 -04:00
ce4d702e25
No-calls and filtered genotypes are now properly considered missing
2011-07-15 14:36:37 -04:00
7b7d40d5d9
A better name for the qscript utilities. Throw here every method you find yourself repeatedly implementing in your qscripts!
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Refactoring appropriately.
2011-07-15 14:34:50 -04:00
a670d6420a
Refactoring Qscript utils into queue general utils package.
2011-07-15 14:31:43 -04:00
28274187e2
Added summary page incorporating core project stats.
2011-07-15 14:22:22 -04:00
c2c8df49e1
Can specify the phasing/child sample on the command-line.
2011-07-15 13:46:24 -04:00
9d59c2cb61
a) Made indel VQSR consensus script operational again, b) Made VariantsToTable more indel-friendly when printing out REF and ALT fields: strip out * from REF and print out alleles in the same way as the VCF so that offline processing is easier
2011-07-15 10:13:02 -04:00
760abf2bc9
Merge branch 'desktop'
2011-07-15 09:38:42 -04:00
f10fa3180e
Bug fix to walker that computes missing genotype error
2011-07-15 09:38:21 -04:00
c5667429a9
Merge branch 'desktop'
2011-07-15 09:28:17 -04:00
c0889df90e
Walker to compute missing genotype error - a metric to assess the quality of imputation
2011-07-15 09:27:04 -04:00
0e9b81283b
Further bug fixes to VQSR indel running script
2011-07-14 20:25:50 -04:00
a36f9c4f6b
Updates to VQSR indel running script
2011-07-14 20:22:58 -04:00
0162426b99
Log chromosome combine job in meaningful file
2011-07-14 19:35:39 -04:00
10cf9245d7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-14 19:18:05 -04:00
9283ac906e
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-14 19:16:46 -04:00
6620ebd8d8
Changes to indel VQSR consensus creation script
2011-07-14 19:16:14 -04:00
f19862a643
Fixing conflicts.
2011-07-14 17:13:31 -04:00
43c6a8565b
looks better now.
2011-07-14 17:10:44 -04:00
09ffe277ae
Added a qscripts util package with some utility functions commonly shared across queue scripts. Refactored some of my public scripts to use it in an effort to make queue scripts more reusable and "supportable".
2011-07-14 17:09:35 -04:00
4f8230c750
Merged bug fix from Stable into Unstable
2011-07-14 16:44:57 -04:00
9f5180ab05
Recalibrates a list of bam files allowing multiple bams to be recalibrated out of a single 'mother' queue job.
2011-07-14 16:42:17 -04:00
04b7f2fc6a
Color scheme consistency. Eliminate density plots that really have no meaning
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(mean target coverage, bad cycles).
2011-07-14 15:16:19 -04:00
c0bbeb23ba
Now providing more information when the index on the fly isn't equal to the one created by reading the file from disk.
2011-07-14 15:12:28 -04:00
5ffeddd3b1
better to use _ instead of ., as this is a special case later.
2011-07-14 14:45:16 -04:00
1f9a730587
Adding density plots to all the existing simple scatter plots.
2011-07-14 14:29:06 -04:00
9540df6998
Oops, forgot to update unit test
2011-07-14 14:00:19 -04:00
ed6beae1f3
Adding headers to diffable reading for VCFs
2011-07-14 13:55:35 -04:00
2d95c71a1c
Integrate mean/sigma markers into generic plotting functions.
2011-07-14 13:49:27 -04:00
2e45f2fb61
Cleanup -- get a lot of the common plotting operations into functions.
2011-07-14 13:13:15 -04:00
57a90173f3
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-14 11:56:20 -04:00
66c652d687
Added some extra error checks in the VCF codec. Now that we've moved this back into the GATK, changed some of the standard exceptions to be USerErrors (instead of TribbleExceptions).
2011-07-14 11:56:10 -04:00
0f568b50fb
Curating the dataset based on 2*sigma filtering, 6 month timestamp.
2011-07-14 09:51:54 -04:00
ad373ffa7e
Broke down and implemented parallel get. Now running 10x parallel no problems on gsa1.
2011-07-14 09:12:43 -04:00
Menachem Fromer
Mauricio Carneiro
Mark DePristo
Roger Zurawicki
Matt Hanna
Guillermo del Angel
Kiran V Garimella
Eric Banks