2fc40a0aed
Fixing the liftover script to not require strict VCF header validation.
...
Apparently no one has used the liftover script for a while (which I guess is a good thing)...
2013-11-07 09:02:17 -05:00
1b10d5467a
Merge pull request #409 from broadinstitute/rp_postQC_titv_ratio_smoothing
...
Smooth over ti/tv bins with small numbers of counts in the PostCallingQC...
2013-10-16 07:41:37 -07:00
e9d0d6ada0
Smooth over ti/tv bins with small numbers of counts in the PostCallingQC script
2013-10-16 10:40:50 -04:00
93d525b56c
Merge pull request #407 from broadinstitute/mc_dwn_exome
...
Qscript to Downsample and analyze an exome BAM
2013-10-10 11:56:12 -07:00
b248a61db6
Merge pull request #408 from broadinstitute/gda_more_pool_caller_stuff
...
PooledCaller paper scripts
2013-10-10 11:55:17 -07:00
36e92a3323
More script committing for posterity -
...
Pool Caller scripts with last minute fixes. Also committed script that plotted 1000G FDR that I used in ASHG2012.
Added also a README.txt file in /humgen/gsa-hpprojects/dev/validationExperiments/largeScaleValidation/finalPaperData/README.txt
in case things need to get run again.
2013-10-10 14:40:12 -04:00
efbfdb64fe
Qscript to Downsample and analyze an exome BAM
...
this script downsamples an exome BAM several times and makes a coverage distribution
analysis (of bases that pass filters) as well as haplotype caller calls with a NA12878
Knowledge Base assessment with comparison against multi-sample calling
with the UG.
This script was used for the "downsampling the exome" presentation
2013-10-10 14:37:33 -04:00
9d932e8c60
Merged bug fix from Stable into Unstable
2013-10-10 14:31:33 -04:00
6f46d1187a
Remember to copy the integration test changes *as well as* the walker changes
2013-10-10 14:30:37 -04:00
55bab9fa87
Merged bug fix from Stable into Unstable
2013-10-10 13:01:12 -04:00
06d28c7f8b
VariantsToBinaryPed: Move .fam file writing to initialize to ensure ordering matches the ordering of the VCF. Change the documentation to clarify that the fam files are not directly copied, but subset and re-ordered.
2013-10-10 12:53:15 -04:00
e9a93d23c3
Merge pull request #405 from broadinstitute/eb_fix_ugcallvariants
...
Don't keep the original QUAL. The whole point of this private walker is to regenerate it!
2013-10-08 08:36:06 -07:00
b71691f5a3
Don't keep the original QUAL. The whole point of this private walker is to regenerate it!
2013-10-08 11:34:14 -04:00
8ebb288014
Auto-restart Bamboo on gsa4 in the event of a crash
2013-10-07 16:10:17 -04:00
385c8d4a70
Place a copy of gsa-engineering's gsa4 crontab under version control
2013-10-07 14:44:56 -04:00
d6fcebf948
Make cron daemon-spawning scripts less chatty
...
Cuts down on gsa-engineering cron emails
2013-10-07 14:35:59 -04:00
49d489cbf8
Merge pull request #393 from broadinstitute/mc_qualify_updates_for_cser
...
Length metric updates to QualifyMissingIntervals
2013-10-04 09:50:39 -07:00
63ace685c9
add unit tests
2013-10-04 11:44:07 -04:00
839b918f58
Length metric updates to QualifyMissingIntervals
...
* add a length of the overlaping interval metric as per CSER request
* standardized the distance metrics to be positive when fully overlapping and the longest off-target tail (as a negative number) when not overlapping
* add gatkdocs to the tool (finally!)
2013-10-04 10:18:13 -04:00
3aef87c214
Merge pull request #403 from broadinstitute/gg_vqsr_disable_plot
...
Disable VQSR tranche plots in INDEL mode
2013-09-30 17:06:51 -07:00
9f7fa247f6
Disable VQSR tranche plots in INDEL mode
2013-09-30 17:14:37 -04:00
749903325e
Merge pull request #404 from broadinstitute/rp_reference_model_bug_fix_blocksize_annotation
...
Bugfix for hom ref records that aren't GVCF blocks.
2013-09-30 06:06:01 -07:00
ef1d58b7ff
Bugfix for hom ref records that aren't GVCF blocks.
2013-09-29 19:19:26 -04:00
f3a67edc24
Merge pull request #402 from broadinstitute/gg_dcov_docs
...
Improvements to gatkdocs related to downsampling
2013-09-27 07:07:21 -07:00
cba9668641
Merge pull request #401 from broadinstitute/gg_vqsr_ignorefilter_doc
...
Minor clarifications regarding ignoreFilter argument
2013-09-27 07:05:41 -07:00
a29f1f84bf
Merge pull request #397 from lbergelson/lb_scala_2.10.2
...
Update scala from 2.9 to 2.10.2
2013-09-26 21:51:43 -07:00
511948890a
Modify gatkdoc template to handle downsampling info better
2013-09-26 14:50:32 -04:00
66d0235efc
Minor clarifications & formatting tweaks for dcov docs
2013-09-26 14:28:22 -04:00
27808d336a
Minor clarifications regarding ignoreFilter argument
2013-09-26 13:13:53 -04:00
a9fa5206ee
Merge pull request #399 from broadinstitute/eb_update_docs_for_DepthPerSampleHC
...
Updated docs for DepthPerSampleHC to deliver PT #54237024 .
2013-09-25 15:20:19 -07:00
f362597f69
Merge pull request #400 from broadinstitute/mm_bugfix_combine_variants_implicit_casting
...
Bug fix: annotation values ar parsed as Doubles when they should be parsed as Integers due to implicit conversion.
2013-09-25 11:47:17 -07:00
5113e21437
Bug fix: annotation values ar parsed as Doubles when they should be parsed as Integers due to implicit conversion.
...
* Updated expected test data in which an integer annotation (MQ0) was formatted as a double.
2013-09-25 13:12:02 -04:00
41fef329b4
Update scripts for depristo -> gsa-engineering migration
2013-09-25 12:57:49 -04:00
2783c84c6b
Updated docs for DepthPerSampleHC to deliver PT #54237024 .
2013-09-24 22:32:19 -04:00
66b51dbc0f
Merge pull request #398 from broadinstitute/eb_update_indel_model_arg_docs
...
Updated docs to tell users not to use PCR indel error modeling for PCR free data.
2013-09-23 12:51:18 -07:00
d6992d1263
Updated docs to tell users not to use PCR indel error modeling for PCR free data.
2013-09-23 15:48:47 -04:00
c05208ecec
Resolving warnings
...
--specifying exception types in cases where none was already specified
----mostly changed to catch Exception instead of Throwable
----EmailMessage has a point where it should only be expecting a RetryException but was catching everything
--changing build.xml so that it prints scala feature warning details
--added necessary imports needed to remove feature warnings
--updating a newly deprecated enum declaration to match the new syntax
2013-09-23 12:42:22 -04:00
b32ad99d3f
Changing from scala 2.9.2 to 2.10.2.
...
--modified ivy dependencies
--modified scala classpath in build.xml to include scala-reflect
--changed imports to point to the new scala scala.reflect.internal.util
--set the bootclasspath in QScriptManager as well as the classpath variable.
--removing Set[File] <-> Set[String] conversions
----Set is invariant now and the conversions broke
--removing unit tests for Set[File] <-> Set[String] conversions
2013-09-23 12:42:22 -04:00
5bbad75402
Changing max coverage threshold
...
Because Integer.maxValue is not unit testable
2013-09-20 18:54:40 -04:00
175388de1d
Merge pull request #396 from broadinstitute/mc_dt_excessive_coverage_defaults
...
Updating excessive coverage default parameter & docs+test for QualifyMissingIntervals
2013-09-20 15:12:16 -07:00
5e2ffc74fc
Automated interpretation for QualifyMissingIntervals
...
* add a new column to do what I have been doing manually for every project, understand why we got no usable coverage in that interval
* add unit tests -- this tool is now public, we need tests.
* slightly better docs -- in an effort to produce better docs for this tool
2013-09-20 16:47:12 -04:00
74639463b9
Updating excessive coverage default parameter
...
most people don't care about excessive coverage (unless you're very
particular about your analysis). Therefore the best possible default
value for this is Integer.maxValue so it doesn't get in the way.
Itemized Changes:
* change maximumCoverage threshold to Integer.maxValue
[delivers #57353620 ]
2013-09-19 23:07:20 -04:00
713c988404
Merge pull request #395 from broadinstitute/dr_chapmanb_patch_add_api_close_methods
...
Provide close methods to clean up resources used while creating AlignmentContexts from BAM file regions
2013-09-11 10:25:54 -07:00
2f5064dd1d
Provide close methods to clean up resources used while creating AlignmentContexts from BAM file regions. Allows utilization of CoveredLocusView via the API
...
Signed-off-by: David Roazen <droazen@broadinstitute.org>
2013-09-10 15:32:54 -04:00
5e539bb11b
Merge pull request #394 from broadinstitute/rp_single_sample_calling_pipeline_update
...
Updates to the single sample calling pipeline to reflect latest experime...
2013-09-10 07:12:05 -07:00
292426b504
Merge pull request #390 from broadinstitute/mc_update_clipreads
...
Added REVERT SOFTCLIPPED bases to ClipReads
2013-09-09 16:43:03 -07:00
8b829255e7
Clarified docs on using clipping options
2013-09-09 19:40:03 -04:00
8971861fd0
Updates to the single sample calling pipeline to reflect latest experiments with full whole genome callsets.
2013-09-09 15:59:50 -04:00
014bc4269e
Merge pull request #361 from broadinstitute/bt_pairhmm_array_implementation
...
Add Array Logless PairHMM
2013-09-08 20:16:53 -07:00
08474a39fb
Merge pull request #389 from broadinstitute/rp_single_sample_calling_pipline_HC
...
Created a single sample calling pipeline which leverages the reference m...
2013-09-06 14:35:51 -07:00
Eric Banks
Ryan Poplin
MauricioCarneiro
Guillermo del Angel
Chris Hartl
David Roazen
Geraldine Van der Auwera
kshakir
Michael McCowan
Louis Bergelson
chapmanb