71046e650e
Added a more robust check for Jishu -- am pretty sure the .bam header is busticated
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4223 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-08 01:11:22 +00:00
ae3f7026a4
Corrected phasing quality evaluation to correctly account for hom sites that break phase
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4222 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-07 22:43:54 +00:00
501f6a0e14
Temporary hack to disable index creation when target BAM is /dev/null. Tim
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promises me that Picard will put in a real solution next week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4220 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-07 16:57:51 +00:00
754c2c761e
Added minimum phasing quality for phasing evaluation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4219 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-07 14:29:11 +00:00
5d0d9c7dce
My parallel version of TranscriptToInfo now emits 'chr start end' instead of 'chr:start-end' for records so that 1) they can be easily sorted in coordinate order (allowing me to emit records out of order if I choose) and 2) the file can be tabix indexed (when we stop finding 'critical' bugs in that code).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4218 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-07 05:20:40 +00:00
4d4ef5b42c
In the end, it's not worth rewriting TranscriptToInfo from scratch. I'm keeping the old one around for a bit so I can play with this new version which 1. doesn't store the records in memory so can be run in under 1Gb of memory, 2. actually emits all of the records (the original fails in some cases), and 3. is refactored to cut out ~20% of the code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4215 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-06 02:37:34 +00:00
0dd5a0990d
Now annotates sites marked as filtered out (this is important if sites are in a lower-quality tranche).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4214 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-04 00:36:55 +00:00
ef7454a241
Minor improvements to indel genotyper:
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a) Ability to specify haplotype size from command line
b) Expand reference context window so we can form haplotypes for longer indel events.
c) small bug fix in temp output writer (to be removed once I can emit vcfs)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4212 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 22:52:08 +00:00
7eeabe534a
QSample walker for 1KG -- measures aggregate quality of sequencing. Includes misc. improvements throughtout the code, including using the new Tribble GenotypeLikelihoods class for working with VCF GLs from the UG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4211 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 18:21:43 +00:00
e3962c0d13
VR integration tests are longer but much more useful.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4210 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 15:50:19 +00:00
da11efa1a2
Automatically write BAM file indices for coordinate-sorted BAMs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4209 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 14:10:44 +00:00
529eecd4dc
Added phasing sub-directory to keep walkers directory clean
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4208 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 13:38:46 +00:00
c0ce9ca8cc
Added phasing sub-directory to keep walkers directory clean
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4207 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 13:32:30 +00:00
60003aeaca
Bug fix in VariantRecalibrator. Only add sample names from the input rod bindings, not from all rod bindings.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4206 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 13:31:49 +00:00
c119f64514
Added phasing sub-directory to keep walkers directory clean
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4205 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 13:24:18 +00:00
3c9597d45a
OnTraversalDone writes output to out now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4203 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 12:55:03 +00:00
73d41bfa24
CountLoci nows writes out to a file for Queue status tracking. VariantAnnotatorEngine has a special group None that doesn't add any annotations; useful for those who are testing UG performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4202 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 12:52:33 +00:00
b59d62927e
Fix busted performance test (-outputBam has been deprecated in the BQ recalibrator in favor of -o)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4201 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 12:51:53 +00:00
70bb480939
The battle is over. Picard is revved.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4200 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 05:28:01 +00:00
fdaac4aa78
As the VCF guru, I'll take this one for Andrey. Someone has actually found a deletion at the beginning of the chromosome. Instead of failing with an ArrayIndexOutOfBoundsException, just don't try to print out the record. Our VCF writer doesn't really support this case (yet).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4199 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 03:27:43 +00:00
c45ffcdaed
Changing documentation (temporarily) to warn people that -U is not supported.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4198 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 03:18:07 +00:00
8a7f5aba4b
First more or less sort of functional framework for statistical Indel error caller. Current implementation computes Pr(read|haplotype) based on Dindel's error model. A simple walker that takes an existing vcf, generates haplotypes around calls and computes genotype likelihoods is used to test this as first example. No attempt yet to use prior information on indel AF, nor to use multi-sample caller abilities.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4197 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 00:25:34 +00:00
a1cf3398a5
Added basic version of phasing evaluation: GenotypePhasingEvaluator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4196 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-02 22:09:50 +00:00
fd5970fdd4
At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.
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No longer generating deprecated GATK arguments on the Queue extensions.
Emitting deprecation warnings to Queue compile to help debugging issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4195 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-02 21:30:48 +00:00
0bb05fb472
Bug fix in VariantRecalibrator. Only add sample names from the input rod bindings, not from all rod bindings.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4194 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-02 21:12:09 +00:00
3a4844ebde
Additional partition types into DepthOfCoverage:
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- Sequencing Center
- Platform
- Sample by Center
- Sample by Platform
- Sample by Platform by Center <---- needed for analysis I'm doing
The fact that the latter three needed their own partition types, rather than being dictatable from the command line, combined with the new hierarchical traversal types, and new output formatting engine, suggest that DepthOfCoverageV3 is about ready to be retired in favor of a newer, sleeker version.
For now, this will do.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4193 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-02 19:30:03 +00:00
590bb50d16
Test for missing read group
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4192 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-02 14:22:13 +00:00
acd6bd2430
Experimental tool to annotates indels that are provided in a VCF file based on RefGene. Specifies gene, transcript, strand, type (Non-frameshift, frameshift, 5'-UTR, 3'-UTR, SpliceSiteDisruption, Intron, or Unknown).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4191 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 23:30:28 +00:00
dc5f858d29
Replaced placeholder support for splitting by read group with read support (sorry everyone), and added relatively comprehensive unit tests to ensure that splitting by read group works.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4190 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 22:24:50 +00:00
b28f63a948
Base recalibrator now uses -o and deprecates -outputBam
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4189 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 22:13:50 +00:00
33400074fa
Updated tribble BED parsing code to use the official UCSC spec, and updated tests to match expected results.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4188 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 21:49:06 +00:00
995cfe34fe
You can have an error so early that some engine fields are uninitialized. Commit protects RunReport from these errors
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4185 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 19:00:25 +00:00
a975db2c2e
Bug fix for the case of reads with no read bases!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4184 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 16:58:54 +00:00
469bbaa240
Added more integration tests for the variant quality score recalibrator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4181 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 15:31:24 +00:00
8c4009ee18
Oops, don't enable reporting in integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4179 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 22:56:18 +00:00
5b94c926c8
More precise language.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4178 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 21:44:22 +00:00
96040726ac
Better exception text for the common error of providing only dbsnp but giving dbsnp sites zero clustering weight.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4177 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 21:36:43 +00:00
32c6b48106
Proper memory metrics in the file. Please use -et if at all possible
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4175 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 20:30:09 +00:00
63c7cbd89b
Forgot to commit this long ago, change so the tables are correctly propagated
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4174 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 19:06:52 +00:00
db4ff7317f
allowing empty RMD files (we need to not validate their sequence dictionaries against the reference in this case)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4173 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 17:45:33 +00:00
3d6c4fc55f
Removing the obsolete --hapmap and --hapmap_chip options
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4172 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 16:57:05 +00:00
b33873206a
GATKRunReport now has an ID (random 32 char string) that uniquely identifies the JOB run and can be used to find a run in the run repository
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4171 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 16:18:57 +00:00
3c956110f3
Fixing up the VCFWriter storage code: instead of assuming all samples are coming from the input bam file (they're not), just use the original VCF header for writing the temporary thread files. Now parallelization in e.g. the Genomic Annotator works.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4168 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 02:16:07 +00:00
69d92fab4f
adding the ability to get iterators from Tribble without having an index, and updating the Tabix code to the latest Samtools SVN version (this still doesn't fix the outstanding tabix bugs, waiting for Heng on that).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4167 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-30 21:49:23 +00:00
50f7f18cbd
Changed ReadBackedPhasing default PQ threshold to 10
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4166 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-30 21:26:15 +00:00
e64d1be475
Check if VC is null before trying to subset it (can happen with indels)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4165 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-30 20:43:37 +00:00
1ddb5d17c9
hostname now fully qualified and working
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4163 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-29 17:04:37 +00:00
4c28fc3a39
Clear documentation for GATKRunReport
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4161 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-29 15:59:25 +00:00
16b75e3b9a
A new version of the ErrorRateByReadPosition walker, using the GATKReport functionality to store and emit its output. This version of the walker is roughly half the number of lines as the previous version, owing simply to the removal of all of the output formatting that's now handled by GATKReport.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4160 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-29 05:41:13 +00:00
fd19c63aaf
A data structure that allows data to be collected over the course of a walker's computation, then have that data written to a PrintStream such that it's human-readable, AWK-able, and R-friendly (given that you load it using the GATKReport loader module).
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This object designed to be both the structure that holds data during the execution of the walker, as well as the object that properly formats and emits the data so that it can be easily loaded into R. In the end, you get a table that looks like this:
##:GATKReport.v0.1 ErrorRatePerCycle : The error rate per sequenced position in the reads
cycle errorrate.61PA8.7 qualavg.61PA8.7
0 0.007451835696110506 25.474613284804366
1 0.002362777171937477 29.844949954504095
2 9.087604507451836E-4 32.87590975254731
3 5.452562704471102E-4 34.498999090081895
4 9.087604507451836E-4 35.14831665150137
5 5.452562704471102E-4 36.07223435225619
6 5.452562704471102E-4 36.1217248908297
7 5.452562704471102E-4 36.1910480349345
8 5.452562704471102E-4 36.00345705967977
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A GATKReport object can hold multiple tables, and the write() method will emit all tables in succession. Each table starts with its own ##:GATKReport.v0.1 table header, so each table can stand alone. This allows for tables to be mixed and matched in a single file, or for the output from different walkers to be combined into a single file with no ill effect.
The display property of individual columns can be turned off. This is useful when a column is used to store intermediate results, necesary for the computation of some later value, but the contents of the intermediate column itself are not required in the final output file.
Finally, the GATKReportTable allows for some simple, mathematical, element-wise and column-wise operations. For instance, two whole columns can be divided, the results of the operation being stored in a third column. This mimics the most basic of R operations, where whole vectors can be added, subtracted, multiplied or divided without requiring the developer to explicitly write a loop.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4159 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-29 05:39:24 +00:00
chartl
fromer
hanna
ebanks
kiran
delangel
depristo
rpoplin
kshakir
aaron