8e149cc52f
Fixing a silly bug of mine: when a realignment target begins at position 1 of a contig, it was possible to have some reads get emitted out of order (triggering an exception in the SAMFileWriter). This is fixed by moving around some parentheses. Tim, if you are reading this: feel free to take this fix in whenever it's convenient. I.e. it's not critical as the only user who has been hit by it has a reference with over 130K short contigs. Committing in SVN so that it gets incorporated immediately (and I can respond on GS now).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6024 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-21 21:42:38 +00:00
6dd41c8489
Nway writer takes another argument: whether to create index on the fly. Realigner in NWayOut mode currently will ALWAYS create index on the fly as there seems to be no clean way to extract the requested value from argument collection in the presence of a different @Output stream.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6023 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-21 17:26:04 +00:00
78461bac1e
Default logic (and name) has changed. Now somatic mode is default one. In order to run in single-sample (unpaired) mode, one has to use (hidden) --unpaired option.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6022 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-21 17:08:41 +00:00
c5de06a641
Fixing up the RefSeqCodec so a bad entry in RefSeq (some transcripts are odd and have a negative length which may signify something special (?) ) doesn't cause failure, but issues a warning instead. Integration tests pass.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6021 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-21 14:07:58 +00:00
7c322780d3
Nway out fixed: in this mode a special nwayout sam writer is instantiated and passed to constrained manager. All the dispatching of the reads into separate output sam streams is taken care by that writer, so no other special processing is needed at the realigner/manager level.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6020 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-20 19:35:26 +00:00
600a6a43a6
Reverting previous commit, as promised.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6019 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-20 16:30:19 +00:00
ee18c9b0c2
Temporary commit to please those in 320: re-support the -knownsOnly argument (@Hidden). This will be reverted in a sec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6018 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-20 16:28:58 +00:00
e8738f95c5
This warning message scares too many people.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6016 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-20 13:43:16 +00:00
4c6d0e6143
Added stratification by discrete allele count, just like AF, but requiring genotypes so it can be exact. Added docs on wiki, and integrationtest using Kiran's very nice fundamental VCF
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VariantEvalWalker now passes a pointer to itself to the Stratefication setVariantEvalWalker (and assoc. get method) so that stratefications can look at VEWalker variables to obtain information necessary for their calculations, like the list of eval samples. This is a better interface, in my opinion, than the current approach of extending the base abstract Stratefication to include an initialize function that has all arguments necessarily for any Strat.
JEXL expressions now provide access to the VariantContext vc object itself, so you can write JEXL's that directly use VariantContext and associated functions from the command line.
ExomePostQC Queue script now creates a byAC eval using the new strat, and no longer produces a byAF file (as this was not exact, and lead to strange punctile behavior when actual AF quantization was out of sync with fix quantization of AF strat.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6015 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-19 03:11:00 +00:00
64196b6c7a
Writer implementation that can dispatch reads to maltiple underlying bam files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6013 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-17 20:44:17 +00:00
1afd24c831
SliceBams now handles properly the case where multiple read groups clash in the input BAM files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6012 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-17 20:19:19 +00:00
dd1d9cd76f
Forgot to deprecate the old args
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6009 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-16 17:54:44 +00:00
4e85416af1
[Foiled yet again when trying to do this in git] Slight modifications in the argument structure for the IndelRealigner. Instead of boolean flags -knownsOnly and -doNotUseSW, we now have an enum --consensusDeterminationModel which lets you specify knowns only, also use indels in reads, or also use SW. Please note that the default behavior of IR has not changed at all (and won't for a few more days) - that'll be done in GIT (fingers crossed).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6008 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-16 17:35:37 +00:00
4304fc4862
Fixed up md5s
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6007 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-16 16:20:41 +00:00
43fdd31e20
Significant performance optimization for reduced reads due to better algorithm for including reads in the variable regions. Fixed a critical bug that actually produced multiple copies of the same read in the variable regions with this optimization as well. Scala exploration script updated as well.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6005 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-16 12:54:59 +00:00
d7430c23f8
Bringing VQSR up to date with the 1000G v2b changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6000 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 20:23:43 +00:00
04ecbf10ab
Fixes the constraint-generated error about stop being less than start in GenomeLocParser.createGenomeLoc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5999 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 17:44:11 +00:00
5be4f31515
Surprisingly, the TileCovariate was indeed covered in integration tests. Updated.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5997 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 17:40:23 +00:00
d00d4fd4d6
Obsolete covariate class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5993 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 14:11:47 +00:00
db43e3f1ab
Fixing an apparent parenthesis matching problem
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5986 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 18:52:14 +00:00
3534f412c9
Better error message for the case of input variants found in ApplyRecalibration that were never seen during VariantRecalibrator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5979 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 14:45:28 +00:00
6231bba288
Bug fix for mergeInfoWithMaxAC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5978 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-12 20:10:16 +00:00
1f4469976e
Made into UserException with better error message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5977 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-12 03:38:52 +00:00
0d6ce91614
When running CombineVariants with -mergeInfoWithMaxAC the set field will be added appropriately
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5974 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-10 14:35:48 +00:00
f8ffda6835
a) Hidden, experimental argument to UnifiedGenotyper that makes code, when in GenotypeGivenAlleles mode, ignore SNP alleles mixed in with indels in complex records - theory is that SNP sites behave statistically differently when doing VQSR so those alleles/sites should be treated separately.
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b) Bug fix: multiallelic indel records where not being treated properly by VQSR because vc.isIndel() returns false with them. Correct general treatment for now is to do (vc.isIndel()||vc.isMixed()).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5973 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-09 19:19:23 +00:00
17e17d3c3c
Misc cleanup in VQSR.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5972 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-09 18:37:37 +00:00
ac3620839c
Very basic intergration tests for ReducedReads, to allow safe optimization of the code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5970 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-09 17:06:32 +00:00
895e86c544
Annotations used to build the 1000G consensus callsets are now standard annotations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5969 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-09 17:03:39 +00:00
93d6e17762
Final, documented version of CalibrateGenotypeLikelihoods.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5966 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-08 20:22:28 +00:00
44287ea8dc
ReducedBAM changes to downsample to a fixed coverage over the variable regions. Evaluation script now has filters and eval. commands.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5965 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-08 19:36:08 +00:00
49b021d435
Changed the definition of degeneracy (it's at the site level - degeneracy of a position in a codon, not degeneracy of the amino acid itself like I initially thought. Added the ability to supply an ancestral allele track (available in /humgen/gsa-hpprojects/GATK/data/Ancestor/).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5963 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-08 15:07:31 +00:00
a331e13721
Slightly more extensive test includes a 0/0 site to genotype
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5961 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-08 14:48:55 +00:00
0f43b10c39
Optimization in CombineVariants when merging into a sites_only VCF
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VariantContextUtils now was a utility function that creates a sitesOnlyVariantContext from an input VC
Add complex merge test of SNPs and indels from the new batch merge wiki in :
http://www.broadinstitute.org/gsa/wiki/index.php/Merging_batched_call_sets
with multiple alleles for an indel. Created a BatchMergeIntegrationTest that uses GGA with the complex merged input alleles to genotype SNPs and Indels with multiple alleles simultaneously in NA12878. Looks great.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5959 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-08 14:31:46 +00:00
1d6486a28f
First part of fix for correctly processing mixed multi-allelic records: correctly compute start/stop of vc when there are no null alleles (i.e. record is not a simple indel).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5958 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-08 13:36:18 +00:00
d27800e07c
a) Forgot to commit this ages ago: uncomment code to ignore hard clipped bases when computing indel likelihoods. b) First part of fix for correctly processing mixed multi-allelic records: correctly compute start/stop of vc when there are no null alleles (i.e. record is not a simple indel).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5957 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-08 11:28:17 +00:00
ad97099df6
Getting rid of a few extra, very explicit qualifications so that the public/
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private bifurcation script doesn't have to discover them.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5956 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-08 03:08:47 +00:00
bb6c0db783
We found the cause of the inconsistency. Woo hoo!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5955 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-07 15:13:58 +00:00
ca48ea78df
At Picard team's request, generate md5s for generated BAM files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5954 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-07 04:25:40 +00:00
311dfa0998
Now builds examples, as I expected. GATKPaperGenotyper lives again.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5953 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-07 00:13:44 +00:00
2901abf070
Switch from PriorityQueue to TreeSet for better and more consistent performance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5952 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-06 20:41:30 +00:00
2c57721ed2
Updated printouts to help with debugging. Issue does appear to be deterministic though.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5950 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-06 01:04:07 +00:00
27dfb53d26
We really don't want to be advising the user to use an unsafe option - really, they should fix their busted bam file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5949 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-05 05:18:16 +00:00
7e49e1668f
Finished changing md5's due to recent change in definition of mixed and indel vc's.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5948 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-05 00:40:51 +00:00
d534241f35
Major revamp of annotations for indels:
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a) All rank sum tests now work for indels including multiallelic sites. For the latter cases, rank sum test is REF vs most common allele
b) Redid computation of HaplotypeScore for indels. It's now trivially easy to do because we are already computing likelihoods of each read vs haplotypes in GL computation so we reuse that if available. For multiallelic case, we score against N haplotypes where N is total called alleles.
Drawback is that all cases need information contained in likelihood table that stores likelihood for each pileup element, for each allele. If this table is not available we dont annotate, so we can only fully annotate indels right now when running UG but not when running VariantAnnotator alone.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5947 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-04 15:34:24 +00:00
1448a1f155
Change md5 because conversion of a tri-allelic dbsnp indel record is now legit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5946 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-04 11:24:16 +00:00
53667ce8fa
Disabled test that checks whether output is the same whether in Genotype Given Alleles mode or not - it won't as long as extended events are finally removed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5945 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-04 00:52:54 +00:00
35df80de14
Updated md5 due to changes to changes in QUAL field when in Genotype given alleles mode w/indels when in insertions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5944 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-03 23:52:38 +00:00
b93829e505
The underlying bam file for this test was busted for many reasons preventing Picard folks from making unrelated changes, so I needed to fix it. Updating md5s accordingly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5943 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-03 22:26:06 +00:00
a8faacda4e
Major change to UG engine to support:
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a) Genotype given alleles with indels
b) Genotyping and computing likelihoods of multi-allelic sites.
When GGA option is enabled, indels will be called on regular pileups, not on extended pileups (extended pileups will be removed shortly in a next iteration). As a result, likelihood computation is suboptimal since we can't see reads that start with an insertion right after a position, and hence quality of some insertions is removed and we could be missing a few marginal calls, but it makes everything else much simpler.
For multiallelic sites, we currently can't call them in discovery mode but we can genotype them and compute/report full PL's on them (annotation support comes in next commit). There are several suboptimal approximations made in exact model to compute this. Ideally, joint likelihood Pr(Data | AC1=i,AC2=j..) should be computed but this is hard. Instead, marginal likelihoods are computed Pr(Data | ACi=k) for all i,k, and QUAL is based on highest likelihood allele.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5941 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-03 22:13:07 +00:00
cd293f145b
More stable reduced reads representation. Bug fixes throughout. No diffs by <1% of sites in an exome, and the majority of these differences are filtered out, or are obvious artifacts. UnitTests for BaseCounts. BaseCounts extended to handle indels, but not yet enabled in the consensus reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5939 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-03 20:11:31 +00:00
ebanks
asivache
chartl
rpoplin
depristo
delangel
kiran
hanna
alecw