2c8d7b0c44
Forgot the onTraversalDone. That was dumb.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2692 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 21:02:46 +00:00
04e1832968
Added - AlleleBalanceHistogramWalker -- hopefully this'll be able to tell us very clearly whether bad genotype concordance is a result of systematic contamination (consistent wonky allele balances)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2691 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 20:57:12 +00:00
a1054efe8a
Default platform and default read group are no longer set to values by default. The recalibrator throws an exception if needed values are empty in the bam file and the args weren't set by the user. This is done to make it more obvious to the user when the bam file is malformed. Similarly, the recalibrator now refuses to recalibrate any solid reads in which it can't find the color space information with an exception message explaining this. The recalibrator no longer maintains its own version number and instead uses the new global GATK version number.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2690 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 18:47:40 +00:00
0345d9f6a5
Updating the recalibrator to use non-depricated getPileup() method. Adding documentation to AnalyzeAnnotations so that the walker isn't marked as unclean at compile time.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2688 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 14:15:09 +00:00
c231547204
Refactoring and migration of new allele/variantcontext/genotype code into oneoffprojects. NOT FOR USE. PlinkRod commented out due to dependence on this new, rapidly changing interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2687 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 13:53:29 +00:00
2e57bc7879
added a better message for the SO flag error in MergingSAMIterator2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2685 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 22:57:18 +00:00
24d4082925
AnalyzeAnnotations can now process only variants that are found in samples that match the -sampleName argument. X-axis of plots no longer use annoying scientific notation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2684 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 20:52:11 +00:00
022601b1a5
Warnings for walkers w/o Javadoc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2683 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 20:34:50 +00:00
894a2b511b
Fixing no platform warning message.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2682 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 19:46:50 +00:00
2b51cf18f0
AnalyzeAnnotations now outputs plots with log x-axis in addition to standard x-axis so things like DP and MQ0 are easier to see. AnalyzeAnnotations now skips over all annotations that aren't floating point values. Recalibrator now warns users if PL tags are missing and so therefore it is reverting to illumina.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2681 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 19:39:18 +00:00
6cf413e630
Bug: ExpandedSAMRecord did not treat hard-clipped bases ('H') correctly. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2680 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 19:23:44 +00:00
dc170caafc
Now, if a dbsnp rod is passed to either the UnifiedGenotyper or VariantAnnotator, a DB=0/1 annotation is added (in addition to filling in the ID field); this is in line with 1KG project calls. If no dbsnp rod is used, the annotation is not added (as opposed to setting every entry to DB=0).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2678 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 17:27:12 +00:00
5d2f8aaa54
Updating recalibrator version number after the several emergency changes last week.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2677 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 14:35:47 +00:00
588417e17d
Don't reference that optimiation library I'm not using anyway.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2676 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-24 20:30:50 +00:00
d3e3c1c2e0
don't require that optmization lib that I'm not using yet... (doh)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2675 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-24 20:28:21 +00:00
1d6d2b26f7
tools for optimizing calls.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2674 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-24 20:16:55 +00:00
877957761f
lots of new stuff, some generally useful, some one-off.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2673 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-24 19:50:48 +00:00
78890c0bee
First version of walker that combines the functionality of IndelIntervalWalker, MismatchIntervalWalker, SNPClusterWalker, and IntervalMergerWalker - plus it allows the user to input rods containing known indels (e.g. dbSNP or 1KG calls) for automatic cleaning. Basically, all pre-processing steps for cleaning are now done in a single pass.
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More testing needed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2672 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-24 05:32:38 +00:00
d6b9b788a8
Renamed -- PlinkRodWithGenomeLoc --> PlinkRod
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Since binary files do not need encoded locus information in the SNP names there's no need to suggest that it is so in the name of the rod
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2671 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 18:19:28 +00:00
ac983e7a0b
Ran the rod on a binary plink file with indels and it just worked. Love it when that happens! Unit test to ensure this behaviour is maintained.
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****** PLINK ROD IS NOW READY TO GO ********
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2670 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 18:13:05 +00:00
ae22d35212
PlinkRod now correctly parses binary files without indels; unit test added for this behavior.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2669 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 17:34:06 +00:00
94dc09c865
PlinkRod now successfully instantiates on the binary ped file trio (.bim, .bam, .fam) for non-indel files.
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Upcoming: Test that the instantiation is correct, do it for indel-containing files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2668 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 16:13:24 +00:00
01db93299c
PlinkRodWithGenomeLoc now properly handels indels.
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There is now a DELETION_REFERENCE allele type to allow for the storage of multi-base references rather than point-mutation references.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2667 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 07:34:52 +00:00
42fb85e7f3
PlinkRodWithGenomeLoc now properly parses text plink files. Unit test added to test this functionality. Indels and binary files to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2666 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 06:19:26 +00:00
c871a0f221
UG map() now returns a VariantCallContext object. Also has a field for confidentlyCalledBases. UG reduce() emits statistics on the confident called % of bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2664 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 23:06:43 +00:00
fbf82526cb
Minor renamign changes.
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PlinkRodWithGenomeLoc now supports .bed file parsing (and doesn't require |c#_p# conventions for SNPs -- still requires _g[I/D] for indels)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2663 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 23:06:32 +00:00
fd223e955c
Reverting the previous solid change. We now refuse to recalibrate if the solid read doesn't contain proper color space information. The exception message has been updated to say this. Also, Tile has been downgraded to an ExperimentalCovariate due to performance issues.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2662 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 20:55:28 +00:00
7732f98e56
Fix for Solid reads that have '.' in their color space field. The recalibrator will just set them to be illumina reads and won't apply color space correction.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2661 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 20:09:16 +00:00
2ea768d902
ant clean is your friend....fixed test code dependent on an interface change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2660 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 20:07:46 +00:00
a11503819a
AnalyzeAnnotations now breaks out its TiTv plots into novel SNPs, dbSNP sites, and combined.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2659 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 19:00:23 +00:00
cc3b818268
cleanup of the pile-up limit exceeded warning, and a little code cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2657 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 22:17:24 +00:00
c1e09efb23
- Fixed output for beagle header
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- Better description for QualByDepth annotation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2655 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 21:25:56 +00:00
d9df72e1b5
AnalyzeAnnotations now bins variants per each annotation and outputs plots of TiTv ratio as a function of the annotation's value.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2654 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 21:15:11 +00:00
f51cffe220
Alteration of PlinkToVCF to be much more flexible about parsing .ped file headers, which can have one of a number of different standard fields, and be in different orders.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2650 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 18:02:28 +00:00
5b2a1e483e
Renamed SequenomToVCF as PlinkToVCF. Wiki will be changed accordingly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2649 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 17:35:20 +00:00
74779a9a78
First version of the tool that tries determining indel error rate (basically, counts indels that look like sequencing/alignment errors - such as a single observation at deeply covered locus, and reports the rate of their occurence)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2648 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 15:28:20 +00:00
d25a2fe120
Better handling of enums by the command-line argument system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2647 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 21:36:46 +00:00
9c7b281b4f
Set default value for max_coverage to be 100K (since 10K is too small).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2646 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 20:15:25 +00:00
1e9fe2a334
Clean up error output when enums have missing arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2645 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 19:48:26 +00:00
8d1d37302c
a quick change to GLF to keep as much precision in our likelihoods as long as possible, before we put it into byte space. Sanger was doing a diff at low coverage and noticed our calls didn't contain as much precision as theirs. Updated the MD5 for unified genotyper output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2644 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 19:36:49 +00:00
908d399670
Bug fix for help text / version number - help text retriever was crashing in the debugger if help text hadn't been built.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2643 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 19:18:19 +00:00
ab289872e4
Changes:
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- Annotations return null when given pileups with no second-base information
- SequenomRodWithGenomeLoc -- beter handling of indels
Eric; I made two small changes to the new Genotype interface that we should talk about (they basically have to do with allele/genotype representation):
Allele - added a new UNKNOWN_POINT_MUTATION to AlleleType. If I see a sequenom genotype AG; one's got to be ref, one's got to be SNP, but until I have
an actual reference base in hand, I don't know which is which. That's what this entry is for.
Genotype - added an enum class StandardAttributes for dealing with things like deletion/inversion length. This is probably not the way we want to
represent indels, so we should talk about this. Plus now that there's a direct link between my ROD and the genotype; when we do decide
how to deal with indels, we'll be forced to alter the SequenomRodWithGenomeLoc accordingly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2642 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 16:45:17 +00:00
a1b4cc4baf
changes to intelligently log overflowing locus pile-ups.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2640 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 08:09:48 +00:00
4ac9eb7cb2
- Smarter strand bias calculation
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- Better debug/verbose printing
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2639 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 03:01:26 +00:00
ff66023d83
Trivial change to support filter field in VCF
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2636 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 22:56:22 +00:00
4625261d79
Bug fix: alignments ending with 'I' were not counted into the overall coverage which resulted in inaccurate stats, and in rare occasions outright messed up ones.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2635 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 22:12:16 +00:00
8dafd26100
Print out the current version number in the application header.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2633 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 21:58:36 +00:00
9e0ae993c7
-B 1kg_ceu,VFC,CEU.vcf -B 1kg_yri,VCF,YRI.vcf system supported to allow 1KG % (like dbSNP%)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2632 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 21:33:13 +00:00
c98df0a862
Updated solid_recal_modes to work with bfast aligned data. Added an integration test that uses the BFAST file provided by TGen.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2630 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 21:18:02 +00:00
53352e1bb4
First pass at a sequenom ROD. Nothing uses it; currently undergoing testing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2629 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 17:09:36 +00:00
chartl
rpoplin
depristo
aaron
hanna
asivache
ebanks
jmaguire