255cc246a2
Change in Methods development pipeline: dbsnp130 can't be used for anything, changed it to dbsnp129. Optimization for HaplotypeScore and the to-be-committed ReadRosRankSumTest in AlignmentUtils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5301 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 16:09:03 +00:00
97e1a5262e
-ct x no longer includes coverage in the previous bin
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BatchMerge - additional support for indels (can't just test the alternate allele when it's an extended event, must also specify that you want to use the dindel model when you actually test the allele)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5300 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 15:52:04 +00:00
ee6f112556
Phase 3: constrained movement is now the only option available in the realigner (so I guess technically it's not really an option). Several command-line options are deprecated. Code cleaned up. Wiki updated. Release coming. One phase left...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5299 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 14:59:48 +00:00
93888e570b
Phase 2: after hours of testing, confirming that constrained mode looks good so moving the integration tests over to use it. Some cleanup. More cleanup coming in Phase 3.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5298 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 06:23:41 +00:00
75bd0129e7
quick bug fix.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5296 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-23 19:16:20 +00:00
9357bee921
Don't skip tri-allelic alleles passed in - just choose the first one.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5293 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-23 17:25:50 +00:00
a2301383bb
quick walker to find out where the reads mapped to huref were mapped in the consensus reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5292 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-23 17:00:17 +00:00
318035c147
Fixing up the output system of the Unified Genotyper. Deprecating the -all_bases and -genotype arguments. Adding instead the --output_mode (EMIT_VARIANTS_ONLY, EMIT_ALL_CONFIDENT_SITES, EMIT_ALL_SITES) and --genotyping_mode (DISCOVERY, GENOTYPE_GIVEN_ALLELES) arguments. UG now does the correct thing when passed alleles (bound to the 'alleles' rod) to use for genotyping; added several integration tests to cover this case. This commit will break the batched calls merging script, but Chris knows this and is ready for it...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5288 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-22 06:07:18 +00:00
d7f98ccd9c
Adding --doNotWriteOriginalQuals argument to BQ recalibrator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5286 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-22 04:00:00 +00:00
1a5d296737
ReplaceReadGroups. Fixes BAM files without read group info. MissingReadGroup points people to this tool now. Please point users on the forum to this tool now. Will migrate to Picard.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5284 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-21 14:02:41 +00:00
cb95e68fc0
CpG is no longer a standard stratification.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5273 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-18 07:17:35 +00:00
9ddee96f93
When subsetting by sample, need to take extra care that hom-ref sites don't accidentally get treated as variant sites in CompOverlap. Renamed convenience method for creating command-lines in integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5272 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-18 06:26:38 +00:00
1bc5c7e99b
boneheaded mistake, mixed up my min and max
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5271 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-18 04:02:14 +00:00
92c82200c9
Fixed an issue where an eval module with TableType objects would get an extra, empty table in the output, screwing up the parse in R.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5267 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-17 23:03:46 +00:00
7ffcade3c3
Added MNP to recognized and counted event types
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5266 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-17 22:37:38 +00:00
57c66b5602
Supports GQ now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5265 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-17 22:30:25 +00:00
f1d708f4d4
Fixes for HRun annotation in case of indels:
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a) In case of a deletion value was completely broken, we'd report 0 or -1.
b) For indels, we report maximum of forward and backward values - I've seen empirically many sites which are not strand biased but which seem to be artifacts and the homopolymer run is always to the right only (because we left align by convention).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5260 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-17 18:57:21 +00:00
0e04e95245
Bug fix: when extracting reference sequence for the event from the reference genome, the tool was treating Deletions and MNPs of length N in exactly the same way: ref_bases[current_pos+1,...,current_pos+N]. This is correct for Deletions but not for MNPs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5258 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-17 16:15:42 +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
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
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
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
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
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
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
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
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
29f3ad72f3
SAMFileWriter that allows the user to move reads, but only a bit, in an incoming coordinated sorted BAM files. Does some local reordering and local mate fixing, under specified constrained. These constrains allow us to make a special -- under testing for Eric, who promised to try this out a bit, expand test cases and integration tests -- but soon to be the default and only model of the realigner that only moves reads with ISIZE < 3000 that directly emits a coordinate sorted, mate fixed validating BAM file without needing FixMates externally. Preliminary testing shows this runs in a totally fine amount of memory and produces equivalent results to the previous version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5199 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 22:27:05 +00:00
03f265d8bd
Change DP format field description in the header line (expected count=1)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5195 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 21:28:25 +00:00
c0e998621c
Computes two format (genotype) level annotations: total read depth in the given sample (DP format field) and fraction of reads supporting alt allele(s) in the given sample (FA format field)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5193 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 21:23:55 +00:00
8700b74640
Now annotates indels as well. Probably can also annotate mixed vcf with indels +snps, but not tested in that mode...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5192 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 20:28:03 +00:00
5c3198520c
A few minor modifications masquerading as significant changes according to
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svn's logs:
- Copied BAM indexing engine from Picard back into the GATK anticipating
shard merging algorithm. Tried to leave most of the building blocks in
Picard. If this turns into a logistical nightmare, I'll merge the building
blocks into the GATK as well.
- Reorganized the org.broadinstitute.sting.gatk.datasources package, giving
better separation of query and management functionality for reads, ref, rmd,
and samples.
- Merged Shard building blocks into org.broadinstitute.sting.gatk.datasources.
reads package, indicating it's current strong relationship with the reads,
rather than the general unifying element I wish this would be.
- Collapsed BAMFormatAwareShard into Shard.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5184 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 17:59:19 +00:00
9ddc95c833
NewEvaluationContext needs to be generated in the inner loop. Otherwise, multiple comp tracks end up getting routed to the same row of the output table. Added test to cover multiple comp tracks.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5181 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 07:04:53 +00:00
918cc09477
Allow multiple records at a position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5178 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 04:19:05 +00:00
cb6454bf98
Multiple eval tracks should be bound with different names, rather than just 'eval'. Added tests to cover usage with multiple tracks.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5177 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 22:33:50 +00:00
5a8e2c2739
Going through the backlog of emergency hacks I put in for the 1000G release. It is possible to call a site in an analysis panel but when using all samples the site isn't called because of going over the minimum deletion threshold, for example.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5174 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 15:12:26 +00:00
2732c839d4
Restored parallelism and associated tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5170 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 02:04:03 +00:00
fd8dd8fb9b
Fixed an issue where a no-call in the eval track would prevent a site from a comparison track from being loaded. Added a new test to cover the use case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5169 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 01:47:53 +00:00
798955b006
After discussing with Mark, revert to "Master merging" of phase information from VCFs. This has the advantage of creating minimal phased VCFs from RBP, from which phase info is merged into the original "master VCF". Also, updated Genotype.sameGenotype() to be simpler and NOT REVERSE the ignorePhase flag in comparing Allele lists/sets
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5167 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 19:50:15 +00:00
dac83d21bc
Fixes for IndelLengthHistogram for someone on GS. This evaluator apparently doesn't have an integration test. I'll fix that tonight.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5166 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 19:48:09 +00:00
e5e65ecfbe
Bugfix for GetSatisfaction: ensure that the two statistics objects (the map, and the pair) are actually pointers to the very same object.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5156 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 06:40:42 +00:00
34f5587f2c
As with the cleaner, don't exception out when trying to get the GATK version after -Ddisable.help=true
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5155 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 06:08:59 +00:00
4243f0dea7
1) Fix for Tim et al: HashMaps don't necessarily return objects in a deterministic fashion when keys are pointers; break it apart into a list.
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2) Fix for Kiran: when running with -Ddisable.help=true, don't exception out when trying to get the GATK version.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5154 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 06:06:48 +00:00
rpoplin
chartl
ebanks
carneiro
depristo
kiran
delangel
asivache
hanna
fromer