c0a4af3809
Expands targets by 50-bp on both sides when the expandIntervals argument is greater than 0.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5251 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-16 14:47:52 +00:00
6d3b878dde
data processing pipeline script already does:
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. Local Indel Realignment
. Mark Duplicates
will do:
. Base Quality Score Recalibration (soon)
it's working with a single BAM for testing, but will work with a list of bam files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5250 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-15 21:49:05 +00:00
5a51c9a815
AWS_S3 logging is now enabled by default. It first tries to log internally at the Broad, and if it can't goes to AWS_S3. DEV option is removed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5249 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-15 20:20:14 +00:00
d2efea6003
This is a draft of the improved and prettified pipeline. It may not yet compile, but Kiran is taking over adding a few more things as I finish up other tasks.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5248 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-15 19:35:00 +00:00
d185c2961f
Added pipeline for calling FCP in batches called MultiFullCallingPipeline.
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Bug smashes for the MCFP:
Synchronized access to LSF library and modifications to the QGraph.
If values are missing from the graph with -run make sure to exit with a non-zero.
Refactored QGraph to pre-generate a unique Int for each QNode speeding up getHashCode/equals inside the graph.
Added jobPriority and removed jobLimitSeconds from QFunction.
All scatter gather is by default in a single sub directory queueScatterGather.
Moved some FCPTest into BaseTest/PipelineTest for use by MFCPTest.
Rev'ed the 1000G bams used for validation from v1 to v2 and added code to look for the bams before running other tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5247 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-15 18:26:14 +00:00
7598f5f6a7
forgot to remove a debug line.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5246 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-15 16:25:48 +00:00
e45b699ac0
standardizing the name of the scripts and fixing some bugs with the remapping.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5245 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-15 16:19:58 +00:00
87e19a17ae
small updates to the variant eval part of the pipeline, some updates to the pacbio specific pipeline.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5244 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-15 16:19:07 +00:00
356eb264ab
Now says FNR, not FDR. We really need to clean up VQSR
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5243 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-15 12:28:09 +00:00
aeee41a755
Fix broken pipeline test (replacing PASS with .)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5242 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-15 02:19:18 +00:00
851b3e71f9
Major revision of the batch merge script. All sites are now used, hooks for some UG settings, no longer reliant on the pipeline management library (pipeline libs are probably going to go away -- nobody uses them)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5241 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-14 23:52:05 +00:00
d6e3f2eba6
Added GC content calculator for CNV data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5240 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-14 22:29:55 +00:00
a081f3b94f
Modifications, bugfix to theoretical posteriors. (Bug fix: eliminated discontinuity in prior distribution)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5239 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-14 19:47:34 +00:00
b8c3c3ae6e
Added commons math, for Kristian.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5238 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-14 18:57:21 +00:00
7a11b4f35d
Another change in variant classification values
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5237 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-14 17:47:58 +00:00
7f7d7eb2d1
Inconsequential changes, more 'variant classification' values are recognized
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5236 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-14 17:36:39 +00:00
d3660aa00e
Very basic functionality for annotating indels (specifies whether the indel is frameshift, inframe, or non-coding). Does not attempt to recalculate the variant codon, variant amino acid, or whether the site falls within a splice region. Added a convenience method to WalkerTest for building command-line arguments with the proper spacing (so that I stop getting annoyed when I've gotten it wrong and the test system yells at me.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5235 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-13 17:58:20 +00:00
8d6db5d188
Additional logging of the temp file creation, management, and merging process
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for VCF files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5234 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-11 22:07:25 +00:00
5f10fffa47
merge intervals now prints a sorted list in the end.
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added the ccs datasets to the pbCalling pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5233 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-11 20:57:59 +00:00
50c2fa3c3a
this -1 made ALL the difference in the world. Minor bug fix.
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Regular updates to the pbCalling pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5232 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-11 19:25:09 +00:00
cdf53188d6
Updated DoC to work with scatter-gather; and, also manually implemented scatter-gather by sample above the scatter-gather by interval. Thansk to Khalid for his support!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5231 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-11 19:14:42 +00:00
e7d38247bb
chunkIntervals.lua creates 1Mb interval chunks out of any .intervals file. Useful for methods development pipeline datasets.
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remapAmplicons.lua takes a sam file with reads aligned to amplicon references, a reference genome , and an amplicon reference mapping table, and rewrites the sam file with mappings to the reference sequence.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5230 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-11 18:21:31 +00:00
03482bf7c4
Number of MQ0 reads in each sample (format field)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5229 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-11 17:16:26 +00:00
8560bb290b
Allelic fractions are now computed on MQ>0 reads only; total depth in each sample still includes MQ0 as per usual convention. Also renamed for clarity.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5228 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-11 17:13:15 +00:00
9554df1a7c
Adding integration test for indels in VF
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5227 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-11 16:58:57 +00:00
c630701a76
Following Ryan's suggestion, I am moving the Methods Development Calling pipeline to the Core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5226 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-10 17:36:05 +00:00
9c2c5efe35
a modified version of the Methods Development calling pipeline made to work with pacbio data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5225 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-10 16:06:50 +00:00
b1e4e1afb6
Slightly better output now -- no longer emitting pdfs by default. Emails will go to gsamembers now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5224 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-10 13:02:24 +00:00
947cc44854
Thanks to Matt for walking me through a proper version of VCF_BAM_utilities! Feel free to add to it, or use it to get the samples in a VCF file, a BAM file, or a collection of BAM files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5223 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-09 18:08:27 +00:00
b992abb6eb
A few more unit tests plus some extra
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functionality for BAM index visualization.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5222 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-09 01:51:34 +00:00
4d1cca95bb
Removed deprecated getDbsnpFile.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5221 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-08 21:12:15 +00:00
a8ab5a5fb9
After code review with APSG, trying a patch for SIGSEGV errors which checks the LSF result codes from lsb_openjobinfo instead of checking for a null return value from lsb_readjobinfo.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5220 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-08 21:08:22 +00:00
f3de9ee3e0
Refactoring of indel evaluation code to make it easier for external functions to get access to indel classification, in preparation for IndelMetricsByAC to stratify indel classes by AC (not done yet).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5219 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-08 17:35:16 +00:00
3635606cd8
Temp checkin just for experimentation: exposed probabilistic alignment parameters to command line interface to make it easier to experiment on their effects, although a full scrap/rewrite of this should be coming soon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5218 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-08 17:33:29 +00:00
e5cfc6ae74
NA12878 hg19 dataset was included to the methods pipeline. (and I am running it)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5217 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-08 16:17:46 +00:00
196eb77699
CG var format is screwed up and doesn't quite fit into the VariantsToVCF mold (we need to see multiple records before we can assign genotypes to a given position), so it's safer to keep this separate from the other well-behaved formats. Hopefully, it's temporary anyways.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5216 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-08 03:18:38 +00:00
4fe0fcd707
Updates to handle CG data, headers, etc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5215 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-08 03:16:05 +00:00
8d0f1b75d5
Added queue/util/BAMutilities Object [with BAM and VCF parsing utilities], which is now used by my qscripts that robustly split runs by sample
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5214 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 22:17:29 +00:00
8040998c15
Renamed the pipeline yaml dbsnpFile to genotypeDbsnp, and added an evalDbsnp.
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Added a genotypeDbsnpType and evalDbsnpType to check the extensions for .vcf or .rod.
Moved renaming of "recalibrated" bams to "cleaned" from sed to yaml generation template (see diff for more info).
Renamed fCP.q to FCP.q.
Though it's still disabled until VariantEval is updated, added changes above to the FCPTest.
Removed refseq table from the queue.sh wrapper script. Only specified in the yaml.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5213 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 22:01:09 +00:00
bceb2a9460
Now that Mauricio has updated the PacBio BAM to properly have RG, can use sample name in the walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5212 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 20:26:57 +00:00
ecbc38aff0
If no comp rod is specified, specify the dummy name none so that we still get counts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5211 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 19:24:52 +00:00
1fbfd4082e
Cycle covariate now works with pacbio reads. No need to override the platform anymore.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5210 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 17:14:55 +00:00
2a04e0d378
Explicitly set logger's level to info - otherwise samtools is too chatty
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5209 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 17:08:50 +00:00
3c1a026c94
Updated script to properly bin DoC values so that down-sampling corresponds to range of DoC values obtainable
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5208 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 16:47:55 +00:00
698096dc5a
Moving VariantsToVCF to the proper directory; removing the oneoffs CG indel converter in preparation for a ligitimate CG variant Feature class in the works.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5207 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 05:21:01 +00:00
35c688ac67
Updated md5 for testVCFStreamingChain to reflect latest changes to VariantEval.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5206 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-06 21:22:05 +00:00
1f820d5026
Added two files from some refactoring changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5205 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-06 19:20:12 +00:00
1085bbf303
Fixed issue where all comp tracks were being treated as known tracks. Fixed issue where multiple JEXL expressions were causing an exception because the underlying object did not implement the Comparable interface. Fixed issue where variants being compared to the known track were not being checked for equality of variation type. Fixed issue where functional annotations were not being iterated over properly. Refactored a lot of helper methods into a separate VariantEvalUtils utility class. Significantly expanded the test suite using a small VCF with SNPs, indels, and non-variant loci which makes it much easier to see what the proper answer should be, and included the appropriate grep and awk commands in the comments to confirm the values.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5204 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-06 19:19:20 +00:00
c4707631e2
MethodsDevelopmentPipeline is now the test bed for large scale AWS_S3 logging. Can be disabled from command line if this is necessary
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5203 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-06 17:03:45 +00:00
8b8b4fced1
Removed explicit memoryLimit, so that memLimit given on the command-line will NOT be ignored...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5202 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-06 01:55:17 +00:00
kiran
carneiro
depristo
corin
kshakir
chartl
fromer
hanna
asivache
ebanks
delangel