d5641cfac5
Merge branch 'variantEvalST'
2011-09-07 10:44:23 -04:00
2f4cf82e3b
VariantEval cleanup. Added VariantType Stratification
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-- ArrayList are List where possible
-- states refactored into VariantStratifier base class (reduces many lines of duplicate code)
-- Added VariantType stratification that partitions report by VariantContext.Type
2011-09-07 10:43:53 -04:00
436f6eb52b
Reverting Eric's change and pushing in some command-line-option documentation.
2011-09-07 08:53:30 -04:00
1ef8a1750a
I asked nicely and got nothing. Then I threatened and still got nothing. So I am carrying through on my threats. Guillermo, you have a short reprieve because you were away on vacation, but let's get yours done tomorrow afternoon.
2011-09-06 21:07:49 -04:00
da9c8ab386
Revving the Tribble jar where the DbsnpCodec class was renamed to OldDbsnpCodec. Updating GATK code accordingly.
2011-09-06 20:39:42 -04:00
9559115ad5
Bugfix for singleton runs. Now with histograms where possible
2011-09-06 16:54:01 -04:00
388d377677
Merge branch 'rrOpt'
2011-09-06 15:11:49 -04:00
3db7ecb920
ReducedRead flag cached in GATKSAMRecord. 20% performance improvement
2011-09-06 15:11:38 -04:00
2d5509e8a6
Now includes the RQ flag in the consensus reads
2011-09-06 15:11:38 -04:00
284f83469b
ReducedRead flag cached in GATKSAMRecord. 20% performance improvement
2011-09-06 15:09:37 -04:00
f3ab7d7c0d
Now includes the RQ flag in the consensus reads
2011-09-06 14:42:27 -04:00
47607a7eff
Fixed bug where deletions messed up interval clipping
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- Instead of using readLength, the ReadUtil function are used to get a proper read coordinate
- Added debug info in interval clipping ( with -dl)
NOTE: method might not be safe for production and checks need to be added to the ClippingOp code
2011-09-06 14:25:57 -04:00
b0b803aa00
Fix for default value of maximum_consensus_base_qual, which can be at most 94
2011-09-06 14:12:54 -04:00
0adb388dee
Fixed bug in SelectVariants that was annotating sample_file / exclude_sample_file as @Argument instead of @Input meaning they weren't tracked in Queue.
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Updates for HybridSelectionPipeline:
- Use VQSR on SNPs for projects using bait set whole_exome_agilent_1 and applying cut at 98.5.
- If a whole_exome_agilent_1 project has less than 50 samples also mixing in 1000G samples to reach VQSR thresholds.
- Updated SNP hard filters based on analysis done with ebanks to approximate VQSR results on small target batches.
- Removed GSA_PRODUCTION_ONLY flag from indel caller.
- Updated indel hard filters based on delangel's analysis.
- Updated HybridSelectionPipelineTest to use HARD SNP filters only, for now.
2011-09-06 12:41:46 -04:00
28d782b4c7
Allowing multiple dnsnp and indel files in the DPP
2011-09-02 13:38:47 -04:00
8da36a965e
Moving the ReadClipping further upstream into the HaplotypeCaller
2011-09-02 13:27:47 -04:00
08ae6c0c61
ReadClipper is now handling unmapped reads
2011-09-02 11:32:30 -04:00
d241f0e903
Adding docs for the pcr error rate argument.
2011-09-01 21:57:02 -04:00
ad4ea0b80b
Merged bug fix from Stable into Unstable
2011-09-01 18:14:45 -04:00
e253f6f05d
Fixing typo in DPP
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platform and library were exchanged when rebuilding the read group information
2011-09-01 18:13:52 -04:00
d2a33beff7
Added WGS/WEX b37-decoy CEU trio datasets
2011-09-01 13:14:40 -04:00
827fe6130c
Adding hidden printing option. Also, always run UG in mode GENOTYPE_GIVEN_ALLELES given that we don't actually test for the correct alleles (otherwise UG may choose a different allele and we may falsely validate the wrong one).
2011-09-01 11:40:35 -04:00
0b794b5491
Reving Tribble to 23
2011-09-01 10:43:03 -04:00
1aa4b12ff0
Reduced the number of combinations being tested here, which was overkill
2011-09-01 10:42:43 -04:00
ac49b8d26b
Conditional support for PerformanceTrackingQuerySource to measure Tribble / GATK bridge performance
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-- Removed DEBUG option, instead use MEASURE_TRIBBLE_QUERY_PERFORMANCE in RMDTrackerBuilder
2011-09-01 10:41:55 -04:00
2b97017871
Fix @Output that should be @Argument
2011-09-01 10:37:20 -04:00
a522488121
First pass at using the indel realigner code to realign reads to the newly assembled haplotypes. Misc bug fix in genotyping engine when both haplotype's alt alleles were deletions.
2011-09-01 09:55:30 -04:00
8529075e60
misc cleanup
2011-08-31 18:53:41 -04:00
70a1ba6fa1
Using ReadClipper to clip the reads instead of manually looking for strings of consecutive high quality bases
2011-08-31 18:52:08 -04:00
f57547ad63
Enabling soft clipped bases in the assembly engine of the haplotype caller
2011-08-31 18:21:56 -04:00
dd89755e74
Merged bug fix from Stable into Unstable
2011-08-31 17:28:44 -04:00
65a9159ac6
Point ivy to the maven repo instead of the default ibiblio repo. Drastically
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simplify ivy config by completely cutting out module specifications.
2011-08-31 17:27:25 -04:00
4b5a7046c5
Making ReadLengthDistribution Public
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Found this neat little walker Kiran wrote stashed in the private tree. Very useful. Generalized it a bit, added GATKDocs and moved it to public. I might include it as a QC step on the pacbio processing pipeline.
* generalize it so it works with non pair ended reads.
* generalize it to work with no read group information
2011-08-31 15:52:28 -04:00
d604019362
Finished my broken tribble code. Updated to rev 22
2011-08-30 16:56:48 -04:00
2585728f03
Fixing the build
2011-08-30 12:45:53 -04:00
bdf04b8057
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-30 11:08:23 -04:00
173ca1e215
Reverting tribble temporarily while I fix my subtle problems
2011-08-30 11:08:13 -04:00
e040ea5c0d
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-30 08:34:01 -04:00
60582215be
Upping the kmer length in order to see larger events
2011-08-30 08:33:49 -04:00
7d79de91c5
Merge branch 'master' into rr
2011-08-30 02:50:19 -04:00
0cd9438ac2
fixed soft unclipped calculation
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* getRefCoordSoftUnclippedEnd was not resetting the shift when hitting insertions. Fixed.
* getReadCoordinateForReferenceCoordinateBeforeAlignmentEnd was returning the wrong read coordinate position. Fixed.
2011-08-30 02:45:29 -04:00
39d8dccc9c
Don't close an empty sliding window
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Sliding window may be empty due to a slide triggered by a previous read that didn't pass the minimum mapping quality filters.
2011-08-30 02:45:20 -04:00
fd540592ab
Added RMS calculation for consensus MQ
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Consensus MQ is now the average of the RMS of the mapping qualities of the reads making each site.
2011-08-30 02:45:20 -04:00
7271998735
Ignore insertions at the beginning of a read.
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Still use the read, but don't mark any base as having insertions for the purpose of the consensus.
2011-08-30 02:45:19 -04:00
f2cc483c22
Adding mapping quality filter to consensus
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only reads > minimum mapping quality are now made into consensus
2011-08-30 02:45:19 -04:00
b2f39fef8e
don't output deletions as bases in the read (consensus)
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The running consensus accepts deletions as long as they are homozygous and (with the current parameters) there is only one read in the pileup. It was generating the cigar string correctly but adding the "D" base to the read bases. Fixed.
2011-08-30 02:45:19 -04:00
dc140b9f18
Fixed window header construction for out of order reads
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Reads can come in out of order due to clipping and the window header may need to have elements added to the head of the list. Fixed.
2011-08-30 02:45:10 -04:00
6f9264d2b3
Hard Clipping no longer leaves indels on the tails
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The clipper could leave an insertion or deletion as the start or end of a read after hardclipping a read if the element adjacent to the clipping point was an indel. Fixed.
2011-08-30 02:44:58 -04:00
943876c6eb
Added QUAL/MINVAR parameters to the walker
2011-08-30 02:44:46 -04:00
c81675be4c
Never allow deletions in the consensus
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This makes it more in line with the insertion treatment and avoids the following problems:
* consensus reads starting with deletions
* variant regions ending abruptly and turning into one consensus with a long insertion, making it difficult to call the deletion in that location.
2011-08-30 02:44:46 -04:00
Mark DePristo
Christopher Hartl
Eric Banks
Roger Zurawicki
Khalid Shakir
Mauricio Carneiro
Ryan Poplin
Matt Hanna
David Roazen