e964660df3
snpSelector now supports min and max q scores.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2751 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-31 19:38:34 +00:00
7b3c34d210
keeping a backup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2750 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-31 15:36:25 +00:00
0fb032a436
Quick script that changes "chr#" to "#" and "chrM" to "MT" and moves mitochondria to the end of the vcf; in accordance with the 1KG reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2727 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-28 21:59:33 +00:00
4990139b60
A collection of python objects that are useful for VCF validation. Use 'em or don't.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2679 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 18:44:10 +00:00
cf46e3c85f
Valuable series of commands
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2641 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 13:58:59 +00:00
8226f4aa12
minor cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2616 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 20:23:20 +00:00
dfe160ff77
Minor changes (additional info calculated)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2522 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 16:41:01 +00:00
588006ee92
Now supports strings in command line for farm submission
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2507 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 13:15:40 +00:00
9fb6533549
new -a option does fast merging of already sorted files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2500 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-05 13:55:39 +00:00
89f3ee614a
minor printing fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2492 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-30 22:14:50 +00:00
fcc80e8632
Completely rewritten duplicate traversal, more free of bugs, with integration tests for count duplicates walker validated on a TCGA hybrid capture lane.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2458 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 23:56:49 +00:00
4e7e0432a2
Updated SNP calling power from coverage tools to work with new UnifiedGenotyper and DepthOfCoverage tools.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2378 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 20:44:30 +00:00
f5e547ed6e
Add ability for flat file table parsing module to skip ahead to first occurence of a regular expression (use case: consistently parsing DepthOfCoverage output for histogram section of file across file format changes)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2377 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 20:38:50 +00:00
bf76019f22
Minor change to coverage evalution script, to update for new file format and add output fields
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2375 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 18:06:08 +00:00
0d2a761460
Bugfix for minBaseQuality to ignore deletion reads. LocusMismatch walker now allows us to skip every nths eligable site
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2357 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 14:38:39 +00:00
56467df49a
minor improvements to snpSelector to work with hapmap chip VCF files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2343 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-13 17:59:32 +00:00
b2dfe85648
Better support for reading truth file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2307 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 12:16:05 +00:00
6a4118ad3c
grr, ought to actually assign it to the TRUTH_CALLS variable
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2302 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 23:31:46 +00:00
987fced151
Should read truth data from the parser options rather than direct from args
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2301 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 23:26:26 +00:00
8825211fdb
Adding this to subversion so it's protected
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2299 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 21:26:17 +00:00
2632cb6b58
minor improvements to snp selector
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2275 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 03:37:14 +00:00
b817db0962
Syzygy has a default LOD score of 0.91 on bases with no coverage, this is problematic. Set the minimum lod threshold to 1 because I just don't want to see that codswallop.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2268 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 23:29:14 +00:00
0753315156
updates to the python snp selector -- now sorts info fields and we stop printing unnecessary debugging info in vcf2table
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2265 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 22:16:02 +00:00
0f89a38473
forgot to commit this earlier
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2264 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 22:10:16 +00:00
c1263e841c
stop printing the debug info -- hurr
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Also it turns out that sometimes there can be a call with zero total non-I/non-D bases -- so add one to numerator and denominator to prevent divide by zero error
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2262 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 16:17:38 +00:00
0c2d6d7e41
A brute-force script to convert Syzygy lod-score calls files into a proper VCF -- with some useful annotations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2261 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 16:07:06 +00:00
2c7cb912f0
Bug fixes for mixed none/valued attributes. also now assigns fake float values for display, if requested, for covariates using the -plottable flag
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2253 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 23:52:35 +00:00
dbb8b86ed1
Minor updates to correctly handle emitting FN calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2231 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 22:53:17 +00:00
67179e2412
Initial checkin of AnalyzeCovariates.java which replaces analyzeRecalQuals_1KG.py and is updated to use the new Covariates system. It creates similar plots of residual error for each covariate that was used in the calculation. There is also an option to filter out base qualities below a given threshold.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2215 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 16:47:35 +00:00
8a87d5add1
misc. bug fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2212 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 14:36:03 +00:00
c93d37d9fb
continuing improvements in output of snpSelector
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2198 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 15:42:06 +00:00
2ea93385be
Better support for comparison to truth. Now emits FP rates for each covariate if a truth file is provided. Also now writes out a detailed recal.log file that can be parsed directly into R
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2179 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-29 22:20:40 +00:00
662bbbd53b
Awful stupid bug. This will use up one of my bad code offsets.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2178 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-29 20:09:33 +00:00
fa2d564f2c
And the compulsory one-second-later fix -- better handling of arguments (e.g. for callng from outside of /trunk/python/)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2177 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-29 20:02:43 +00:00
45673d7851
A quick and dirty script that, given a list of input VCF files, will output a new VCF file which looks identical to the first VCF file of the input list, except that the info field has been updated to reflect the union of all the INFO annotations across the VCF files
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Note: this is primarily for use with two files with mostly disjoint annotations. It views "SB=2.5" as a different info field than "SB=2.2" and so will output as info "SB=2.5;SB=2.2". That is, it compares the full field string, rather than only the field name.
Usage:
./mergeVCFInfoFields I=[comma-delimited list of files] O=[output file]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2176 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-29 20:01:29 +00:00
65da04ca85
Now uses the theoretically correct relationship between SNP FP and TP ratios for Illumina data. maxQ score for a snp is now 60
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2168 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 22:08:12 +00:00
03342c1fdd
Restructuring and interface change to ReadBackedPileup. We now lower support the Pileup interface, the BasicPileup static methods, and the ReadBackedPileup class. Now everything is a ReadBackedPileup and all methods to manipulate pileups are off of it. Also provides the recommended iterable() interface of pileup elements so you can use the syntax for (PileupElement p : pileup) and access directly from p.getBase() and p.getQual() and p.getSecondBase(). Only a few straggler walkers use the old style interface -- but those walkers will be retired soon. Documentation coming in the AM. Please everyone use the new syntax, it's safer, and will be more efficient as soon as the LocusIteratorByState directly emits the ReadBackedPileup for the Alignment context, as opposed to the current interface. In the process of the change over, discovered several bugs in the second-best base code due to things getting out of sync, but these changes were resolved manually. All other integrationtests passed without modification.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2154 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 03:51:41 +00:00
bc35a34f60
More informative printing, no longer prints tons of NaN warnings
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2139 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 15:45:48 +00:00
da7de9960b
General bug fixes for snpSelector. More robust error checking and handling of NaN values.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2106 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-21 14:48:29 +00:00
52494d8176
cleanup of SNP selector -- ready for some additional testing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2042 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 21:46:31 +00:00
1a4d071d37
Better snpSelector, plus VCFmerge tool
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2022 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-11 22:02:57 +00:00
3990c6d950
snpSelector v3 -- bootstrapping support and VCF output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2004 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 22:48:51 +00:00
f777c806d6
snpSelector v2 -- code refactoring and support for comparison with known truth. Looks great.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1986 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-07 19:32:12 +00:00
7cb51dbc31
snpSelector v1 -- and supporting changes to VCF reader
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1983 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-06 23:00:46 +00:00
eca0942644
Oops. Let's make sure only to write calls that the pool supports to the auxiliary vcf files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1974 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-04 17:14:55 +00:00
fc17e75759
Put this puppy through its paces. Eliminated the sorting and header-handling stuff; that isn't the purvey of this script and should be handled downstream or by a script wrapper.
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I also secretly handled another pesky overlow exception. Occasionally Syzygy could report lods of like -1000; e.g. posterior probabilities of one in one (((googol) googol) googol) googol which of course makes python blow up. Now we safely output an accurate posterior.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1971 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-04 06:05:45 +00:00
3d9195f8b6
Added - converter from expanded summary to VCF (beautiful thing, really)
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Removed - the ugly hackjob that was expanded summary to Geli
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1970 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 22:20:47 +00:00
d60c632099
Minor output improvement
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1965 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 13:20:55 +00:00
44ea55d338
Useful library for parsing VCF files, plus a general VCF->table converter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1964 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 13:14:04 +00:00
99337df929
Now looks up and propagates Syzygy's LOD scores into the appropriate field (so variantfiltration can adjust lod scores accurately)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1950 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 21:13:03 +00:00
depristo
chartl
andrewk
rpoplin