0e8536f5f3
Adding the ability to add multiple kmer lengths in the debruijn graph.
2011-09-07 19:17:45 -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
7532be7f5a
Allowing to clip after AlignmentEnd if end is soft clipped.
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Read clipper now identifies and clips even if the requested coordinate is outside the alignment but the read contains soft clipped bases in that region.
2011-08-30 02:44:46 -04:00
90a1f5e15c
Several bug fixes
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* When hard clipping a read that had insertions in it, the insertion was being added to the cigar string's hard clip element. This way, the old UnclippedStart() was being modified and so was the calculation of the new AlignmentStart(). Fixed it by subtracting the number of insertions clipped from the total number of hard clipped bases.
* Walker was sending read instead of filtered read when deleting a read that contains only Q2 bases
* Sliding the window was causing reads that started on the new start position to be entirely clipped.
2011-08-30 02:44:19 -04:00
66a8b36cf5
Fixed most indexing bugs
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* added bases and quals to consensus
* fixed consensus read cigar generation.
2011-08-30 02:43:41 -04:00
6a4a47568c
Added sample script for generating per sample metrics and updated the queue.sh used for running pipelines to be renamed.
2011-08-29 22:10:35 -04:00
077b6a58da
Merging (un-merging?) reverts into unstable. Current unstable uses "leftAligned" while current stable does not use "leftAligned".
2011-08-29 20:09:48 -04:00
5fdd10340a
Merged bug fix from Stable into Unstable
2011-08-29 20:08:04 -04:00
cf2430322a
Manually fixing unintentional path changes for dbsnps.
2011-08-29 20:06:28 -04:00
2125ba1f23
Merged bug fix from Stable into Unstable
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Conflicts:
private/java/src/org/broadinstitute/sting/pipeline/ReferenceData.java
2011-08-29 19:36:43 -04:00
20ac24464d
Rev'ved picard to read new analysis_files.txt with a blank line after header and no reference sequence.
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Updated error messages and unit tests.
2011-08-29 19:33:04 -04:00
427c643ce7
The missing tribble jar
2011-08-29 18:46:40 -04:00
c6d8df8639
queueJobReport is a public feature of Queue
2011-08-29 17:20:54 -04:00
1e5001b447
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-29 17:04:21 -04:00
5defaf5fac
Continuing to improve Tribble
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-- ProfileRodSystem now has a just load index mode, allowing us to optimize the profiler
-- assessFarmNodes R script for making nice plots of performance of jobs on the farm
-- Rev. tribble to use new, optimized index loading (performance win when loading many many indices)
2011-08-29 17:02:57 -04:00
3af001fff2
Bugfix for file that must not exist on disk
2011-08-29 17:00:10 -04:00
Ryan Poplin
Mauricio Carneiro
Eric Banks
Mark DePristo
Matt Hanna
David Roazen
Khalid Shakir