85626e7a5d
We no longer want people to use the August 2010 Dindel calls for indel realignment but instead Guillermo's new whole genome bi-allelic indel calls; updating the bundle accordingly. Also, there was some confusion by the 1000G data processing folks as to exactly what these indel files are, so I've renamed them so that it's clear. Wiki updated too.
2011-09-19 12:24:05 -04:00
ca1b30e4a4
Fix the -T argument in the DepthOfCoverage docs
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Add documentation for the RefSeqCodec, pointing users to the wiki page describing how to create the file
2011-09-19 10:29:06 -04:00
7fa1e237d9
Forgot to git stash pop new MD5's for CombineVariants integration test
2011-09-16 12:53:54 -04:00
e7b9a009b7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-16 12:48:30 -04:00
42f3b7ba32
Merged bug fix from Stable into Unstable
2011-09-16 12:46:38 -04:00
33967a4e0c
Fixed issue reported by chartl where cloned functions lost tags on @Inputs.
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Updated ExampleUnifiedGenotyper.scala with new syntax.
2011-09-16 12:46:07 -04:00
92f7db3228
Can now optionally suppress the use of all annotations and then add back in specific annotations/groups. This was necessary, since using all annotations for VariantAnnotator NOW includes SNPeff, which (annoyingly) requires a SNPeff VCF...
2011-09-16 02:40:24 -04:00
b2e8e11128
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-16 00:52:27 -04:00
3cd9f3fe81
Merge remote-tracking branch 'unstable/master'
2011-09-15 21:14:17 -04:00
57b3efa2e2
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-15 21:06:38 -04:00
939babc820
Updating formating for ValidationAmplicons GATK docs
2011-09-15 21:05:51 -04:00
9fdf1f8eb6
Fix some doc formatting for Depth of Coverage
2011-09-15 21:05:22 -04:00
e6e9b08c9a
Must provide alleles VCF to UGCallVariants
2011-09-15 18:51:09 -04:00
1960bcabb8
Updated to use new ROD-binding system
2011-09-15 18:07:32 -04:00
d78e00e5b2
Renaming VariantAnnotator SnpEff keys
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This is to head off potential confusion with the output from the SnpEff tool itself,
which also uses a key named EFF.
2011-09-15 17:42:15 -04:00
1971fb35d7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-15 16:55:33 -04:00
9dc6354130
Oops didn't mean to touch this test before
2011-09-15 16:55:24 -04:00
2a8b8efd2f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-15 16:26:35 -04:00
2f58fdb369
Adding expected output doc to CountCovariates
2011-09-15 16:26:11 -04:00
fd1831b4a5
Updating docs to include more details
2011-09-15 16:25:03 -04:00
6d02a34bfb
Updating docs to include output
2011-09-15 16:17:54 -04:00
4ef6a4598c
Updating docs to include output
2011-09-15 16:10:34 -04:00
fe474b77f8
Updating docs so printing looks nicer
2011-09-15 16:05:39 -04:00
f04e51c6c2
Adding docs from Andrey since his repo was all screwed up.
2011-09-15 15:38:56 -04:00
ce73dc4071
Update to the bindings for liftOverVCF.pl (to -V from -B)
2011-09-15 15:33:09 -04:00
7d6b34b1bb
Can now optionally annotate with a dbSNP VCF
2011-09-15 15:31:38 -04:00
86480b2e13
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-15 15:31:07 -04:00
04f5723399
Updated to use new ROD-binding system
2011-09-15 14:28:06 -04:00
d369d10593
Adding documentation before the release for GATK wiki page
2011-09-15 13:56:23 -04:00
202405b1a1
Updating the FunctionalClass stratification in VariantEval to handle the snpEff annotations; this change really needs to be in before the release so that the pipeline can output semi-meaningful plots. This commit maintains backwards compatibility with the crappy Genomic Annotator output. However, I did clean up the code a bit so that we now use an Enum instead of hard-coded values (so it's now much easier to change things if we choose to do so in the future). I do not see this as the final commit on this topic - I think we need to make some changes to the snpEff annotator to preferentially choose certain annotations within effect classes; Mark, let's chat about this for a bit when you get back next week. Also, for the record, I should be blamed for David's temporary commit the other day because I gave him the green light (since when do you care about backwards compatibility anyways?). In any case, at least now we have something that works for both the old and new annotations.
2011-09-15 13:52:31 -04:00
1e682deb26
Minor html-formatting-related documentation fix to the SnpEff class.
2011-09-15 13:07:50 -04:00
a942fa38ef
Refine the way we merge records in CombineVariants of different types. As of before, two records of different types were not combined and were kept separate. This is still the case, except when the alleles of one record are a strict subset of alleles of another record. For example, a SNP with alleles {A*,T} and a mixed record with alleles {A*,T, AAT} are now combined when start position matches.
2011-09-15 10:22:28 -04:00
3db457ed01
Revert "Modified VariantEval FunctionalClass stratification to remove hardcoded GenomicAnnotator keynames"
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After discussing this with Mark, it seems clear that the old version of the
VariantEval FunctionalClass stratification is preferable to this version.
By reverting, we maintain backwards compatibility with legacy output files
from the old GenomicAnnotator, and can add SnpEff support later without
breaking that backwards compatibility.
This reverts commit b44acd1abd9ab6eec37111a19fa797f9e2ca3326.
2011-09-14 10:47:28 -04:00
e0c8c0ddcb
Modified VariantEval FunctionalClass stratification to remove hardcoded GenomicAnnotator keynames
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This is a temporary and hopefully short-lived solution. I've modified
the FunctionalClass stratification to stratify by effect impact as
defined by SnpEff annotations (high, moderate, and low impact) rather
than by the silent/missense/nonsense categories.
If we want to bring back the silent/missense/nonsense stratification,
we should probably take the approach of asking the SnpEff author
to add it as a feature to SnpEff rather than coding it ourselves,
since the whole point of moving to SnpEff was to outsource genomic
annotation.
2011-09-14 07:09:47 -04:00
1213b2f8c6
SnpEff 2.0.2 support
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-Rewrote SnpEff support in VariantAnnotator to support the latest SnpEff release (version 2.0.2)
-Removed support for SnpEff 1.9.6 (and associated tribble codec)
-Will refuse to parse SnpEff output files produced by unsupported versions (or without a version tag)
-Correctly matches ref/alt alleles before annotating a record, unlike the previous version
-Correctly handles indels (again, unlike the previous version
2011-09-14 07:09:47 -04:00
5b1bf6e244
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-13 17:04:43 -04:00
c6672f2397
Intermediate (but necessary) fix for Beagle walkers: if a marker is absent in the Beagle output files, but present in the input vcf, there's no reason why it should be omitted in the output vcf. Rather, the vc is written as is from the input vcf
2011-09-13 16:57:37 -04:00
64707c33bb
Merged bug fix from Stable into Unstable
2011-09-12 21:54:11 -04:00
e63d9d8f8e
Mauricio pointed out to me that dynamic merging the unmapped regions of multiple BAMs ('-L unmapped' with a BAM list)
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was completely broken. Sorry about this! Fixed.
2011-09-12 21:50:59 -04:00
4e116760f4
Removing some old cruft from the packages dir. Updating AnalyzeCovariates to include all Covariates.
2011-09-12 15:09:25 -04:00
ec4b30de6d
Patch from Laurent: typo leads to bad error messages.
2011-09-12 14:45:53 -04:00
9d9d438bc4
New VariantAnnotatorEngine capability: an initialize() method for all annotation classes.
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All VariantAnnotator annotation classes may now have an (optional) initialize() method
that gets called by the VariantAnnotatorEngine ONCE before annotation starts.
As an example of how this can be used, the SnpEff annotation class will use the initialize()
method to check whether the SnpEff version number stored in the vcf header is a supported
version, and also to verify that its required RodBinding is present.
2011-09-12 13:00:53 -04:00
981b78ea50
Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts.
2011-09-12 12:17:43 -04:00
60ebe68aff
Fixing issue in VariantEval in which insertion and deletion events weren't treated symmetrically. Added new option to require strict allele matching.
2011-09-12 09:43:23 -04:00
07d365ce39
Fixing units in queue job report Gantt plots
2011-09-12 09:01:34 -04:00
09050a01db
Adding qscript to run the HaplotypeCaller in parallel
2011-09-11 22:53:40 -04:00
30be6d8bd6
Removing the copy of the original assembler since it has been successfully assimilated
2011-09-11 21:00:27 -04:00
9344938360
Uncomment code to add deleted bases covering an indel to per-sample genotype reporting, update integration tests accordingly
2011-09-10 19:41:01 -04:00
b399424a9c
Fix integration test affected by non-calling all-zero PL samples, and add a more complicated multi-sample integration test from a phase 1 case, GBR with mixed technologies and complex input alleles
2011-09-09 20:44:47 -04:00
e95d484757
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-09 18:31:14 -04:00
Eric Banks
Christopher Hartl
Guillermo del Angel
Khalid Shakir
Menachem Fromer
David Roazen
Ryan Poplin
Matt Hanna