f15355856a
Merge pull request #418 from broadinstitute/eb_fix_liftover_script
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Fixing the liftover script to not require strict VCF header validation.
2013-11-07 06:04:56 -08:00
2fc40a0aed
Fixing the liftover script to not require strict VCF header validation.
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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
f67c3a1b4e
Merge pull request #415 from broadinstitute/eb_new_path_for_NIST_in_kb_upload
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Various updates to the knowledge base
2013-11-06 13:00:45 -08:00
23c9c24adc
Various updates to the knowledge base
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1. Updated NIST path to its proper place on the file system (and updated the NIST calls to the latest, v2.17).
2. Don't assess genotype concordance for multi-allelic sites because we mess up the GTs when we break
them into their component parts (and therefore the GTs look wrong when they really aren't).
3. Add an argument to control the minimum GQ for a GT to be considered called.
This improves genotyping accuracy assessments which were unfairly penalizing low confidence GT calls.
Delivers PT #59846158 .
2013-11-06 14:05:07 -05:00
0e3d83d1ef
Merge pull request #413 from broadinstitute/rp_qd_and_qual_updates_in_ref_model_pipeline
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Improvements to the reference model pipeline.
2013-11-05 06:33:17 -08:00
09dfaf1a68
Merge pull request #416 from broadinstitute/mc_quick_fixes_to_cser_pipeline
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Add interpretation to QualifyMissingIntervals
2013-11-05 06:08:13 -08:00
a372c0f074
Merge pull request #414 from broadinstitute/eb_update_dbsnp_in_bundle
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Update the dbsnp version in the bundle from 137 to 138; resolves PT #59771004 .
2013-11-04 07:04:23 -08:00
96024403bf
Update the dbsnp version in the bundle from 137 to 138; resolves PT #59771004 .
2013-11-04 10:01:22 -05:00
b22c9c2cb4
Improvements to the reference model pipeline.
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-- We use the RegenotypeVariants walker to recompute the qual field. (instead of the discussed idea of adding this functionality to CombineVariants)
-- QualByDepth will now be recomputed even if the stratified contexts are missing. This greatly improves the QD estimate for this pipeline. Doesn't work for multi-allelics since the qual can't be recomputed.
2013-11-01 17:58:25 -04:00
cafcb34855
Merge pull request #411 from broadinstitute/eb_add_exome_intervals_to_bundle_script
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Updated the GATK bundle script to:
2013-10-29 07:38:44 -07:00
209f2a61aa
Updated the GATK bundle script to:
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1. Include exome target list for b37
2. Not delete the 'current' link unless -run is applied to the command line! (sorry, Ryan)
2013-10-29 10:33:51 -04:00
0ad23c09d5
Merge pull request #410 from lbergelson/lb_missing_script_error
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Improving the error message for a missing Queue script.
2013-10-25 08:57:06 -07:00
5ed47988b8
Changed the parameter names from cds to baits
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Making the usage more clear since the parameter is being used over and over to define baited
regions. Updated the headers accordingly and made it more readable.
2013-10-24 17:15:56 -04:00
9498950b1c
Adding more specific error message when one of the scripts doesn't exist.
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--Previously it gave a cryptic message:
----IO error while decoding blarg.script with UTF-8
----Please try specifying another one using the -encoding option
2013-10-21 14:57:42 -04:00
5a2ef37ead
Tweak dcov documentation to help prevent user confusion
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Geraldine-approved!
2013-10-16 15:24:33 -04:00
1b10d5467a
Merge pull request #409 from broadinstitute/rp_postQC_titv_ratio_smoothing
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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
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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
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PooledCaller paper scripts
2013-10-10 11:55:17 -07:00
36e92a3323
More script committing for posterity -
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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
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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
5d6421494b
Fix mismatching number of columns in report
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Quick fix the missing column header in the QualifyMissingIntervals
report.
Adding a QScript for the tool as well as a few minor updates to the
GATKReportGatherer.
2013-10-09 14:38:15 -04:00
e9a93d23c3
Merge pull request #405 from broadinstitute/eb_fix_ugcallvariants
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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
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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
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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
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* 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
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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
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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
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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
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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
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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
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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
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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.
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* 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
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Updated docs to tell users not to use PCR indel error modeling for PCR free data.
2013-09-23 12:51:18 -07:00
Eric Banks
amilev
Ryan Poplin
kshakir
Mauricio Carneiro
Louis Bergelson
David Roazen
Guillermo del Angel
Chris Hartl
Geraldine Van der Auwera
Michael McCowan