zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
1,509 Commits
1 Branch
0 Tags
257 MiB
Commit Graph

590 Commits (ada4c5a13cee8abba445fc8cdd99b66add8bfc3e)

Author SHA1 Message Date
ebanks 43f63b7530 Added a walker to convert a bam file to fastq format (including the option to re-reverse the negative strand reads). 
Picard has such a tool but it is geared towards their pipeline and requires intimate knowledge of the lanes/flowcells,etc.  This is just easy.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1413 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-12 15:10:40 +00:00
asivache e4acd14675 Now GenomicMap maps (and RemapAlignment outputs) regions between intervals on the master reference as 'N' cigar elements, not 'D'. 'D' is now used only for bona fide deletions. 
Also: do not die if alignment record does not have NM tags (but mapping quality will not be recomputed after remapping/reducing for the lack of required data)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1411 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-11 21:10:17 +00:00
ebanks 5fab934f4e - moved the reference maker to its own directory 
- added first version of a more complicated reference maker which takes in RODs and creates an alternative reference based on the variants (indels and/or SNPs)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1409 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-11 18:01:06 +00:00
sjia 1851613de4 Now using larger database of HLA alleles 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1405 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-11 03:11:14 +00:00
asivache 3208eaabcc A standalone picard-level tool for breaking individual reads into "pairs" of first/last N bases. Supports: 
* splitting off only start or end of the read, or both; the output will contain 
     chopped sequences AND corresponding base qualities
   * splitting arbitrary number of bases off each end (different numbers
     for left and right segments can be specified; segments can overlap)
   * splitting only unmapped reads, ignoring mapped ones
   * writing splitted ends into separate sam/bam files, or into a single output file
   * decorating original read names with user-specified suffixes for each end
     (e.g. _1 and _2 for left and right parts of the read); default: no decoration, 
     original read names are used
   *  when mapped reads are split, the alignment cigars are chopped appropriately
     and the alignment start positions are adjusted (for the right end) to correctly 
    specify the alignment of the selected part of the read


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1402 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-10 20:42:49 +00:00
asivache 36312ae4b2 tiny cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1401 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-10 20:26:52 +00:00
asivache 921d4f4e95 RemapAlignments is a standalone picard-level tool that does not use gatk engine; moved to 'tools' 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1396 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-10 15:41:07 +00:00
depristo 089dab00e2 Was discordance rate, now concordance rate 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1393 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-07 19:37:52 +00:00
depristo 6d3ef73868 Now includes statistics on the allele agreement with dbSNP -- counts concordant calls as dbSNP = A/C and we say A/C, vs. we say A/T 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1392 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-07 19:37:07 +00:00
depristo a864c2f025 Updated polarized reference priors, need DiploidGenotypePriors class that is directly used by the NewHotness genotypelikelihoods, more bug fixes and refactoring, etc. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1390 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-07 19:00:06 +00:00
ebanks db250f8d3e Don't print if not in learning mode 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1389 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-07 06:08:02 +00:00
ebanks 4c1fa52ddf -Added mapping quality zero filter 
-Set some reasonable defaults (based on pilot2)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1388 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-07 03:18:02 +00:00
sjia d60d5aa516 Fixed bug: previously reset likelihoods after each region/exon. 
Better comments/documentation added

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1386 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-05 18:44:46 +00:00
kcibul 0d47798721 made booster distance a parameter 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1385 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-05 18:29:21 +00:00
ebanks 3b74b3ba74 print out ref/alt ratio, not major/minor 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1384 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-05 16:36:25 +00:00
depristo 65e9dcf5b7 Fully operational version of the new genotype likelihoods class. (1) Much cleaner interface. Now explicitly stores likelihoods, priors, and posteriors in separate arrays indexed by an enum, (2) no longer can be used to make calls, it relies on SSGGenotypeCall to order the likelihoods, calculate best to ref, etc, this is just for calculating genotype likelihoods now; (3) Now performs extensive error checking with validate() to ensure the system is behaving properly. (4) fixed incorrect treatment of N bases, which we being counted against everyone (5) likely found a stats bug in which heterozyosity was being applied incorrectly to the genotype priors 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1382 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-05 01:00:55 +00:00
sjia 68309408e4 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1378 348d0f76-0448-11de-a6fe-93d51630548a 2009-08-04 21:23:01 +00:00
sjia 45ab212f22 Post-presentation update 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1377 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-04 21:21:12 +00:00
hanna 21d1eba502 Cleaned division of responsibilities between arguments to map function. Reference has been changed 
from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-04 21:01:37 +00:00
kcibul a5a7d7dab8 added "booster" metrics 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1375 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-04 20:53:45 +00:00
ebanks 3a8d923785 minor output changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1374 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-04 20:12:16 +00:00
mmelgar 939b19e715 Committing the first version of the homopolymer filter. Removes SNPs that occur at the edges of homopolymer runs and whose nonref allele matches the repeated base in the homopolymer. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1373 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-04 14:35:51 +00:00
depristo 20ff603339 New hotness and old and Busted genotype likelihood objects are now in the code base as I work towards a bug-free SSG along with a cleaner interface to the genotype likelihood object 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1372 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-03 23:07:53 +00:00
depristo 3485397483 Reorganization of the genotyping system 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1370 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-03 20:55:31 +00:00
ebanks 9f1d3aed26 -Output single filtration stats file with input from all filters 
-move out isHet test to GenotypeUtils so all can use it


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1369 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-03 20:44:21 +00:00
depristo d840a47b11 Slight reorganization of genotype interface 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1366 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-03 19:17:15 +00:00
depristo 20986a03de cleanup before moving files 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1365 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-03 19:08:24 +00:00
ebanks e3b08f245f Pull out RMS calculation into MathUtils for all to use 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1364 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-03 17:00:20 +00:00
ebanks e495b836d3 - added mapping quality filter 
- make the filters brainless in that they strictly have thresholds and filter based on them; require user to calculate and input these thresholds.
- update filters in preparation for migration to new output format



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1363 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-03 16:46:51 +00:00
kiran 8bc925a216 Commit on the behalf of Mark: cleaning up some old and busted code in GenotypeLikelihood and associated objects. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1361 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-31 21:18:30 +00:00
aaron 9dfee7a75c the "-genotype" option now acts correctly as a discovery mode caller in SSG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1359 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-31 18:31:45 +00:00
sjia 9dada95ec3 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1357 348d0f76-0448-11de-a6fe-93d51630548a 2009-07-31 16:21:16 +00:00
andrewk 678c2533ca Removed custom output stream for file and replaced with the standard out PrintStream 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1350 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-30 22:36:42 +00:00
andrewk 44673b2dce Removed a debugging println that was accidentally checked in 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1348 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-30 22:23:27 +00:00
andrewk 845488ff94 VariantEval now decides whether a variant is not confidently called using BestVsNetxBest if genotypes are being evaluated and BestVsRef if not (variant discovery only). Also, the absolute value of the BestVsRef LOD (getVariantionConfidence) is used so that confident reference calls (if the GELI has output them) will show up in the final table as reference calls rather than no calls. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1347 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-30 21:54:06 +00:00
andrewk fdc7cc555b Removed extra column name from geliHeaderString that was mislabeling the 10 genotype likelihoods by shifting them over by onex 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1345 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-30 21:42:02 +00:00
aaron 0087234ed7 small code cleanup, a couple of little changes to SSGGenotypeCall 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1343 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-30 19:47:37 +00:00
ebanks fbc7d44bc7 don't allow users to input priors anymore; they should be using heterozygosity and having the SSG calculate priors. 
Note that nothing was changed for dnSNP/hapmap priors (not sure what we want to do with these yet - any thoughts?)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1342 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-30 19:10:33 +00:00
ebanks b282635b05 Complete reworking of Fisher's exact test for strand bias: 
- fixed math bug (pValue needs to be initialized to pCutoff, not 0)
- perform factorial calculations in log space so that huge numbers don't explode
- cache factorial calculations so that each value needs to be computed just once for any given instance of the filter

I've tested it against R and it has held up so far...



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1341 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-30 18:52:13 +00:00
aaron 4033c718d2 moving some code around for better organizations, some fixes to the fields out of SSG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1340 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-30 15:09:43 +00:00
ebanks 4366ce16e0 Made sure all RODs have a (good) toString() method - and use it in the Venn walker. (thanks, Mark) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1339 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-30 14:53:27 +00:00
aaron 9cd53d3273 some initial changes from the first review of the genotype redesign, more to come. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1338 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-30 07:04:05 +00:00
hanna 5429b4d4a8 A bit of reorganization to help with more flexible output streams. Pushed construction of data 
sources and post-construction validation back into the GATKEngine, leaving the MicroScheduler
to just microschedule.  


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1336 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-29 23:00:15 +00:00
aaron bca894ebce Adding the intial changes for the new Genotyping interface. The bullet points are: 
- SSG is much simpler now
- GeliText has been added as a GenotypeWriter
- AlleleFrequencyWalker will be deleted when I untangle the AlleleMetric's dependance on it
- GenotypeLikelihoods now implements GenotypeGenerator, but could still use cleanup

There is still a lot more work to do, but this is a good initial check-in.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1335 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-29 19:43:59 +00:00
kiran c5c11d5d1c First attempt at modifying the VFW interfaces to support direct emission of relevant training data per feature and exclusion criterion. This way, you could run the program once, get the training sets, and then feed that training set back to the filters and have them automatically choose the optimal thresholds for themselves. This current version is pretty ugly right now... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1334 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-29 19:29:03 +00:00
ebanks 3554897222 allow filters to specify whether they want to work with mapping quality zero reads; the VariantFiltrationWalker passes in the appropriate contextual reads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1333 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-29 17:38:15 +00:00
hanna 7a13647c35 Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very* 
rough initial implementation, but should provide enough support so that people can stop
creating SAMFileWriters in reduceInit.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1332 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-29 16:11:45 +00:00
depristo 56f769f2ce Output improvements to GenotypeConcordance calculations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1331 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-29 12:54:46 +00:00
ebanks 72dda0b85c Fixed calculations for Mark 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1330 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-29 03:21:43 +00:00
ebanks f0378db9b7 added accuracy numbers 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1329 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-29 01:38:33 +00:00
ebanks a5a56f1315 At this point, we are convinced that the new priors are the way to go... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1328 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-28 17:25:25 +00:00
depristo df4fd498c5 Improvements and bug fixes galore. (1) Now properly handles Q0 bases, filtering them out, you can disable this if you need to (2) support for three-state base probabilities (see email), which is disabled by default (still experimental) but appears to be more emppowered to detect variants (see email too) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1327 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-28 13:21:38 +00:00
depristo 46643d3724 Improvements and bug fixes galore. (1) Now properly handles Q0 bases, filtering them out, you can disable this if you need to (2) support for three-state base probabilities (see email), which is disabled by default (still experimental) but appears to be more emppowered to detect variants (see email too) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1326 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-28 13:21:27 +00:00
ebanks 3c4410f104 -add basic indel metrics to variant eval 
-variants need a length method (can't assume it's a SNP)!


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1324 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-28 03:25:03 +00:00
kcibul 1d6d99ed9c walk by reference 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1323 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-27 20:21:04 +00:00
ebanks 089ae85be7 1. output grep-able strings for genotype eval 
2. free DB coverage from isSNP restriction


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1322 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-27 17:36:59 +00:00
kcibul 1bca9409a4 calculate freestanding intervals 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1321 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-27 16:40:27 +00:00
asivache 2499c09256 added minIndelCount (short: minCnt) command line argument. The call is made only if the number of reads supporting the consensus indel is equal or greater than the specified value (default: 0, so only minFraction filter is on in default runs!) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1320 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-27 15:22:51 +00:00
ebanks 73ddf21bb7 SNPs no longer fail this filter if they are actually hom in reads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1319 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-27 15:20:43 +00:00
asivache f2b3fa83ac fix for another bug found by Eric: some indels were printed into the output stream twice (when there's another indel within MISMATCH_WINDOW bases and that other indel requires delayed print in order to accumulate coverage) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1318 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-27 15:07:07 +00:00
asivache 5eca4c353c IndelGenotyper now uses GATK::getMergedReadGroupsByReaders() to sort out which read in the merged stream is for normal, and which is for tumor (in --somatic mode, apparently) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1316 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-24 23:01:18 +00:00
asivache 64221907a2 fixed a bug found by Eric: genotyper would crash in the case of an indel too close to the window end, with the next read mapping sufficiently far away on the ref 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1313 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-24 21:00:31 +00:00
hanna df44bdce7d Retire the pooled caller...its been eclipsed by other walkers in the tree. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1310 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-24 14:49:03 +00:00
kiran 884806fc16 Broken and unused. It goes away now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1309 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-24 14:26:52 +00:00
ebanks d044681fbe change paths to new ones 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1308 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-24 07:28:43 +00:00
ebanks 59f0c00d77 -set indel cleaning walkers to be in core package 
-move Andrey's alignment utility classes to core


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1307 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-24 05:23:29 +00:00
kiran bb20462a7c A better way: down-scale second-base ratios until the infinities disappear. This way, high-coverage sites don't cause binomialProbability to explode. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1306 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-24 03:02:00 +00:00
kiran 038cbcf80e If the result from the secondary-base test is 0.0, replace the result with a minimum likelihood such that the log-likelihood doesn't underflow. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1303 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-23 20:59:52 +00:00
kiran 093550a3f2 Removed secondary-base test from SingleSampleGenotyper. It now lives in the variant filtration system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1302 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-23 20:58:41 +00:00
ebanks 477502338f moved major indel cleaning pieces to core (yippee!) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1301 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-23 19:59:51 +00:00
ebanks 4efe26c59a Major: allow genotyper to optionally output in 1KG format, including outputting the samples in which indels are found. 
Minor: refactor 454 filtering


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1300 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-23 19:53:51 +00:00
ebanks f8b1dbe3b3 getBestGenotype() does not necessarily return hets in alphabetical order; 
the string (unfortunately) needs to be sorted for lookup in the table (otherwise we throw a NullPointerException)
TO DO: have the table be smarter instead of sorting each genotype string


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1298 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-23 01:58:47 +00:00
ebanks ee8ed534e0 print full genotype for alt allele 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1297 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-23 01:35:23 +00:00
depristo 9c12c02768 AlleleBalance and on/off primary base filters -- version 0.0.1 -- for experimental use only 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1294 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-22 17:54:44 +00:00
ebanks c54fd1da09 Beautify the genotype concordance printouts 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1291 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-22 02:53:02 +00:00
hanna 1843684cd2 Cleanup: GATKEngine no longer needs to be lazy loaded, b/c the plugin directory no longer exists. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1287 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 18:50:51 +00:00
hanna b43925c01e Switched to Reflections (http://code.google.com/p/reflections/) project for 
inspecting the source tree and loading walkers, rather than trying to roll
our own by hand.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1286 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 18:32:22 +00:00
kiran 436a196e2b Bug fixes to support hapmap genotyping concordance. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1285 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 16:20:10 +00:00
depristo 7e04313b4e Bug fixes and improvements to CoverageHistogram. Now displays the frequency of the bin. Also correctly prints out the last element in the coverage histogram (<= vs. <) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1284 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 11:55:05 +00:00
aaron b4adb5133a GLF rod as a AllelicVariant object. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1282 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 00:55:52 +00:00
kiran f314ef8d84 Features and exclusion criteria are now instantiated in VariantFiltrationWalker's initialize() method, rather than in every map() call. This means the features and exclusion criteria will only ever be initialized once. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1281 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-20 22:47:21 +00:00
mmelgar 8da754eb4e First implementation of a primary base filter. Assumes distribution of on/off bases is distributed according to a binomial. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1278 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-17 18:43:35 +00:00
ebanks 24ebfee604 don't print traversal stats 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1277 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-17 16:13:28 +00:00
ebanks f978b04633 A very simple walker to print out (using the ROD's toString method) all of 
the RODs it sees.  This is the easiest solution to get around the (temporary)
bug of reads being seen multiple times by reads walkers when close intervals
are passed to them (i.e. process full contigs and then use a ref walker to
filter the ones within your intervals of choice)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1273 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-17 14:03:34 +00:00
hanna df1c61e049 Re-add the plugin path. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1271 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-16 22:48:44 +00:00
hanna 7c30c30d26 Cleaned up some duplicate code in preparation for making plugin dir configurable. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1270 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-16 22:02:21 +00:00
depristo 31f3f466ca Improvements to support GLF generation -- now correctly handles GLF 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1269 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-16 21:10:39 +00:00
depristo 0548026a2e Now understanding GLFs for calculating genotyping results like callable bases, as well as avoids emitting stupid amounts of data when doing a genotype evaluation (i.e., ignores non-SNP() calls) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1267 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-16 21:03:26 +00:00
depristo c5f6ab3dd5 CoverageHistogram now sees 0 coverage sites 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1266 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-16 20:58:41 +00:00
ebanks 8bc0832215 Generate chip concordance table. 
This should work, although I need to test it with some real GLFs


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1265 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-16 17:44:47 +00:00
kcibul e1055bcc4c moving to new external repository 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1261 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 20:46:08 +00:00
kcibul 4a730adfc1 committing latest changes before moving repositories 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1260 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 20:44:02 +00:00
ebanks a245ee32fa A walker to split 2 call sets into their intersection/union/disjoint (sub)sets. 
Yes, the name is retarded, but I'm under pressure here...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1258 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 20:20:47 +00:00
kcibul 00d49976fb committing latest changes before moving repositories 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1255 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 18:41:52 +00:00
aaron 9ecb3e0015 adding GLFRods with tests and some other code changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1251 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 15:30:19 +00:00
hanna c25f84a01c Regression: we lost our hack to work around BAM files with index problems (affects BAM files created before 23 Apr 2009 and traversed by interval). Added the hack back in, along with a much more explicit comment about why its there. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1248 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 14:41:37 +00:00
depristo 1798aff01b VariantEval now understands the difference between a population-level analysis and a genotype analysis, and handles both. All analyses annotated as supporting one or the other or both. Preparation for genotype chip concordance calculations as well as called sites, etc analyses 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1247 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 14:07:13 +00:00
depristo 84d407ff3f Fixing odd merge problem with VariantEval -- better cluster analysis (no cumsum), rodVariant is now an AllelicVariant 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1239 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-14 18:53:27 +00:00
aaron 7d755a4c90 GenotypeLikelihoods doesn't emit metrics, they don't make sense 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1236 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-14 17:22:28 +00:00
aaron 01fc8da270 adding the GenotypeLikelihoodsWalker, which generates GLF genotype likelihoods that are pretty much identical to the samtools calls. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1235 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-14 16:57:18 +00:00