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
71680e3fd6
Extremely minor tweaks to the GSAPipelineIndexer
2011-08-29 16:55:54 -04:00
3b09d42ed6
Now only prints 1 warning message about duplicate headers in simpleMerge
2011-08-29 14:41:29 -04:00
c2f0db969b
Don't use the default deletion value from UG if not asking to have it set
2011-08-29 13:48:10 -04:00
bb7a37e8f2
We need to allow reference calls in the input VCF for the GenotypeAndValidate walker when using the BAM as truth so that we can test supposed monomorphic calls against the truth.
2011-08-29 13:19:35 -04:00
5b56c83401
Don't output variants that on the edges of the haplotype, far away from the original interval.
2011-08-29 11:15:07 -04:00
661d658a0e
Updating smith-waterman parameters for the general case of aligning both with indels and snps simultaneously
2011-08-29 09:49:34 -04:00
bc252a0d62
misc minor bug fixes in assembly. Increasing the minimum number of bad variants to be used in negative model training in the VQSR
2011-08-29 08:11:31 -04:00
f9afc5876a
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-29 08:04:39 -04:00
61633c95a8
Default jobreport is now jobPrefix, so you see logs like Q-2508.jobreport.txt
2011-08-28 19:19:45 -04:00
a5c65fc133
Debugging information to print out the Query tracks
2011-08-28 18:54:49 -04:00
d1b2b4ece9
Simple R script to analyse node performance
2011-08-28 16:40:38 -04:00
796ba34f6d
Simple script that can be used to access farm node performance
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-- spawns bundle dbsnp countrod that takes ~15 minutes to complete in general
-- import cleanup for RodPerformanceGoals
2011-08-28 15:09:50 -04:00
7542d29507
Oops, enabling default displays again
2011-08-28 12:07:38 -04:00
84704aaee3
Support for exechosts. Only displays by default in the gantt chart as jobname @ exechosts.
2011-08-28 12:06:41 -04:00
Ryan Poplin
Matt Hanna
Mauricio Carneiro
Mark DePristo
David Roazen
Khalid Shakir
Eric Banks