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
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
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
dd1810140f
-stratIntervals is optional
2011-11-10 13:27:32 -05:00
67b022c34b
Cleanup for new SampleUtils function
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-- getVCFHeadersFromRods(rods) is now available so that you don't have getVCFHeadersFromRods(rods, null) throughout the codebase
2011-11-10 13:27:13 -05:00
9490d71bc8
Folding recent HMM changes into Haplotype Caller. Misc bug fixes throughout HC.
2011-11-10 13:26:29 -05:00
35fe9c8a06
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-10 11:11:33 -05:00
714cac21c9
Testdata for IntervalStratification
2011-11-10 11:08:34 -05:00
dc4932f93d
VariantEval module to stratify the variants by whether they overlap an interval set
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The primary use of this stratification is to provide a mechanism to divide asssessment of a call set up by whether a variant overlaps an interval or not. I use this to differentiate between variants occurring in CCDS exons vs. those in non-coding regions, in the 1000G call set, using a command line that looks like:
-T VariantEval -R human_g1k_v37.fasta -eval 1000G.vcf -stratIntervals:BED ccds.bed -ST IntervalStratification
Note that the overlap algorithm properly handles symbolic alleles with an INFO field END value. In order to safely use this module you should provide entire contigs worth of variants, and let the interval strat decide overlap, as opposed to using -L which will not properly work with symbolic variants.
Minor improvements to create() interval in GenomeLocParser.
2011-11-10 10:58:40 -05:00
0d8983feee
outputting the RG information
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setReadGroup now sets the read group attribute for the GATKSAMRecord
2011-11-09 23:35:00 -05:00
315ac68b0b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-09 22:37:36 -05:00
6313aae2c4
Adding checks for hasBasePileup() before calling getBasePileup() as per GS thread
2011-11-09 22:37:26 -05:00
74a18d3de8
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-09 22:29:40 -05:00
24712c0221
Merged bug fix from Stable into Unstable
2011-11-09 22:28:27 -05:00
8942406aa2
Use MathUtils to compare doubles instead of testing for equality
2011-11-09 22:05:21 -05:00
348f2db7fd
Fix for HMM optimization. If the two penalty arrays match exactly the function should return the end of the array instead of 0.
2011-11-09 22:00:52 -05:00
9a4486a9e6
BaseCounts now include N's
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Fixing unit tests accordingly.
2011-11-09 21:29:33 -05:00
82bf09edf3
Mark Standard Annotations with an asterisk
2011-11-09 20:42:31 -05:00
04b122be29
Fix for bug reported on GetSatisfaction
2011-11-09 20:33:36 -05:00
d00b2c6599
Adding a synthetic read for filtered data
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* Generalized the concept of a synthetic read to cread both running consensus and a synthetic reads of filtered data.
* Synthetic reads can now have deletions (but not insertions)
* New reduced read tag for filtered data synthetic reads *(RF)*
* Sliding window header now keeps information of consensus and filtered data
* Synthetic reads are created simultaneously, new functionality is controlled internally by addToSyntheticReads
2011-11-09 20:16:22 -05:00
3afbd0e526
Sliding Window Header now includes filtered data information
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This is a necessary framework for the filtered data consensus reads to be produced.
2011-11-09 20:16:22 -05:00
6ee90ada14
Quick optimization to the SlidingWindow builder
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from O(n^2) to O(n). Not bad.
2011-11-09 20:16:21 -05:00
21bf43f3bb
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-09 15:34:40 -05:00
02d5e3025e
Added integration test for intervals from bed file
2011-11-09 15:34:19 -05:00
85bffe1dca
Merged bug fix from Stable into Unstable
2011-11-09 15:29:14 -05:00
d828eba7f4
Allow comments in a table-formatted file to precede the header line.
2011-11-09 15:27:38 -05:00
8205efbb29
Merge branch 'master' into intervals
2011-11-09 15:27:15 -05:00
Eric Banks
Guillermo del Angel
Mauricio Carneiro
Ryan Poplin
Mark DePristo
Christopher Hartl