457c59e737
Use the sites-only HapMap files in the Methods development pipeline
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5013 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-18 20:50:09 +00:00
35a4f1e366
.Added VariantEval as an optional step in the pipeline.
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.Lifted to HapMap 3.3
.Lifted to dbSNP 132 where possible.
.Added the CEU-Trio WEx(hg19) dataset
.Added some options to the pipeline
You can now use :
-dataset WEX
-dataset HiSeq
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to choose which datasets to run through the pipeline.
You can now without BAQ and indel mask:
-noBAQ
-noMASK
Choose not to run the gold standard comparison analysis:
-skipGoldStandard
Activate the VariantEval walker analysis on the Recalibrated vcf:
-eval
The default behavior is to run exactly like it used to, so this version shouldn't change the way you used to use the pipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5004 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-14 21:55:02 +00:00
20f29e4690
In the Methods development pipeline the call confidence threshold must be lowered from the default value for lowpass calling. What a bone-headed mistake!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4941 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 20:30:55 +00:00
7185fcb47b
Committing my notes about the methods development pipeline so we stay synced up while I'm on vacation. Cheers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4891 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-21 21:14:20 +00:00
4ca1da1d07
Updating the NA12878.HiSeq bam file to be the correct bam file in the methods development qscript.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4879 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 14:53:10 +00:00
8fac346ac1
Misc cleanup in Methods Development Qscript
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4878 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 04:24:25 +00:00
34ab5b4889
Turning on BAQ in Methods Development pipeline. A new dataset is added: 363 EUR samples from the November 1000G release.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4877 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-19 21:13:25 +00:00
15a33545f4
Updating Methods development pipeline qscript with the bam lists for all the data sets. It is ready for people to start running with it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4875 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-18 22:19:14 +00:00
bdef4e775a
Initial checkin of methods development pipeline qscript. It allows the methods dev team to run an overnight job which calls and recalibrates a variety of data sets and allows for an end-to-end sanity check of final results for potential changes to the methods. It isn't meant to be used by anybody quite yet, but shows the general structure and flow.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4871 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 22:14:02 +00:00
rpoplin
carneiro