e7d41d8d33
Minor cleanup
2011-11-17 12:00:28 -05:00
f250b47228
Someone broke this for SNPs when adding support for indels
2011-11-16 10:49:27 -05:00
eb8e031f75
Merged bug fix from Stable into Unstable
2011-11-16 09:57:37 -05:00
6a5d5e7ac9
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/stable
2011-11-16 09:57:13 -05:00
7ac5cf8430
Getting rid of unsupported CountReadPairs walker in stable. Removal of
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remainder of pairs processing framework to follow in unstable.
2011-11-16 09:53:59 -05:00
c2ebe58712
Merge remote-tracking branch 'Laurent/master'
2011-11-16 09:34:47 -05:00
7d77fc51f5
Corrected bug causing PhaseByTransmission to crash in case of new Genotype.Type
2011-11-16 03:32:43 -05:00
0d163e3f52
SnpEff 2.0.4 support
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-Modified the SnpEff parser to work with the SnpEff 2.0.4 VCF output format
-Assigning functional classes and effect impacts now handled directly
by SnpEff rather than the GATK
-Removed support for SnpEff 2.0.2, as we no longer trust the output of that
version since it doesn't exclude effects associated with certain nonsensical
transcripts. These effects are excluded as of 2.0.4.
-Updated unit and integration tests
This support is based on a *release-candidate* of SnpEff 2.0.4, and so is subject
to change between now and the next GATK release.
2011-11-15 18:36:22 -05:00
fb685f88ec
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-15 16:23:53 -05:00
7fada320a9
The right fix for this test is just to delete it.
2011-11-15 14:53:27 -05:00
231b8e9f74
Do not output deletion only synthetic reads
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If a synthetic read is composed exclusively of deletions, do not output it.
2011-11-15 13:24:43 -05:00
b45d10e6f1
The DP in the FORMAT field (per sample) must also use the representative count or else it's always 1 for reduced reads.
2011-11-15 10:23:59 -05:00
b66556f4a0
Update error message so that it's clear ReadPair Walkers are exceptions
2011-11-15 09:22:57 -05:00
cde829899d
compress Reduce Read counts bytes by offset
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compressed the representation of the reduce reads counts by offset results in 17% average compression in final BAM file size.
Example compression -->
from : 10, 10, 11, 11, 12, 12, 12, 11, 10
to: 10, 0, 1, 1,2, 2, 2, 1, 0
2011-11-14 18:30:24 -05:00
a1ce3d8141
Not reporting counts to reduced deletions (temporary patch)
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Deletions will not have counts represented in the reduced form. This may change in the future with a ReadBackedPileup refactor.
2011-11-14 18:30:24 -05:00
ab0ee9b847
Perform only necessary validation in VariantContext modify methods
2011-11-14 16:49:59 -05:00
5c38a9cfd6
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-14 15:00:03 -05:00
f1db31f072
Attempt to reduce memory footprint of ValidationSiteSelector (if this doesn't work then a radical rewrite of the walker to make it two-pass will be necessary): don't log any attributes of original VCF, if we need chr counts later we can reannotate from original inputs. As things stand, we can't select SNP's genomewide due to memory usage.
2011-11-14 14:56:09 -05:00
4dc9dbe890
One quick fix to previous commit
2011-11-14 14:42:12 -05:00
b3313e1445
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-14 14:31:38 -05:00
7b2a7cfbe7
Transfer headers from the resource VCF when possible when using expressions. While there, VA was modified so that it didn't assume that the ID field was present in the VC's info map in preparation for Mark's upcoming changes.
2011-11-14 14:31:27 -05:00
509ecc62cc
Another bug fix for when no samples are specified in ValidationSiteSelectionWalker
2011-11-14 13:02:51 -05:00
7aee80cd3b
Fix to deal with reduced reads containing a deletion
2011-11-14 12:23:46 -05:00
3d2970453b
Misc minor cleanup
2011-11-14 09:41:54 -05:00
1347beef40
Merge branch 'PhaseByTransmission'
2011-11-14 11:31:28 +01:00
6881d4800c
Added Integration tests for Phasing by Transmission
2011-11-14 10:47:51 +01:00
34acf8b978
Added Unit tests for new methods in GenotypeLikelihoods
2011-11-14 10:47:02 +01:00
b7c33116af
Minor docs update
2011-11-12 23:21:07 -05:00
76d357be40
Updating docs example to use -L since that's best practice
2011-11-12 23:20:05 -05:00
af8e39c04d
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-12 08:42:24 -05:00
c95f015d77
a) Bug fix in validation site selector, b) Initial qscript for selection of random snps and indels for validation experiment
2011-11-12 08:41:53 -05:00
8cd077f009
Writing a GATKReport table as output.
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just to standardize the output.
2011-11-11 18:52:58 -05:00
cd3146f4cf
Add hidden option to ValidationAmplicons to output slightly modified format to make file work with downstream SQNM tools more seamlessly at request of GAP: one line per record, keep probe identifier to 20 characters, no * in ref allele.
2011-11-11 14:07:07 -05:00
40fbeafa37
VQSR will now detect if the negative model failed to converge properly because of having too few data points and automatically retry with more appropriate clustering parameters.
2011-11-11 11:52:30 -05:00
59945a41e8
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-10 23:05:20 -05:00
0c32281484
Adding a benchmarking class for parsing VCF files. Not complete.
2011-11-10 23:05:13 -05:00
9c013374fd
A walker to calculate the coverage of a target
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in targeted sequencing projects, we pay a penalty to get to a minimum coverage in 80% of the targets. This walker will help us understand what is the ratio between the targeted site (usually in the middle of the interval) and the targeted region.
2011-11-10 17:16:51 -05:00
ffa6bc66ec
Eliminating excessive debug tests
2011-11-10 17:16:51 -05:00
5a1170078a
Using centralized reduce read facilities
2011-11-10 17:16:51 -05:00
dc9b351b5e
Meaningful error message when an IntervalArg file fails to parse correctly
2011-11-10 17:10:26 -05:00
bb7bf74aa8
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-10 16:05:43 -05:00
153e52ffed
VariantEvalIntegrationTest for IntervalStratification
2011-11-10 14:10:39 -05:00
060c7ce8ae
It wouldn't harm integrationtests if we had our logic right... :-)
2011-11-10 14:03:22 -05:00
bb4cd59475
Filtered and consensus reads will now use the same tag
2011-11-10 13:58:31 -05:00
7a46273d75
Consensus reads had filtered data read names
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fixed.
2011-11-10 13:58:31 -05:00
c14b182501
Add reads in the recursive call
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was missing consensus reads that got added from the recursive call. This is was a side-effect of the filtered data implementation. Fixed.
2011-11-10 13:58:31 -05:00
07dbf0bd40
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-10 13:39:24 -05:00
26762d6c6f
Folding recent HMM changes into Haplotype Caller. Misc bug fixes throughout HC.
2011-11-10 13:36:03 -05:00
39678b6a20
Check for reads with missing read groups and throw a UserException when encountered. Mauricio said this wouldn't break integration tests.
2011-11-10 13:34:45 -05:00
18f829f76b
Towards a full G1KPhaseI table creation script
2011-11-10 13:27:54 -05:00
Eric Banks
Matt Hanna
Laurent Francioli
David Roazen
Mauricio Carneiro
Guillermo del Angel
Ryan Poplin
Mark DePristo