d92055d1f9
Checkpointing some bugfixes with zero-length version directories and missing
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Picard metrics files before the push back into svn.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6069 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:56:01 +00:00
f7fa373643
Incorporate lists of fingerprint data rather than summaries.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6044 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:54:23 +00:00
e0d203434f
Add a column summing the fingerprint LOD scores.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6041 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:54:09 +00:00
751aa8bfa6
Partial rewrite of the summary metrics aggregator to accumulate all metrics
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from sample-level summaries, rather than only specific metrics. Continues to
manually handle fingerprinting.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6038 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:53:53 +00:00
4288ca1c24
Fix doc bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6037 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:53:49 +00:00
cc1f94310d
A prototype script and library dependencies to extract a BAM list from a
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reasonably well-formed PM's xls{x}-format spreadsheet or tsv file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6036 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:53:45 +00:00
69f5f16711
Added conditional checking for median_insert_size.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6029 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 17:59:54 +00:00
14d7ee073b
Rev Picard to get new PF_INDEL_RATE metric. Rev preQC generator script
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to incorporate PF_INDEL_RATE.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5998 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 17:43:43 +00:00
7aec71f0e1
Add some very simple documentation on running and modifying the per-sample
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metrics generator.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5995 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 15:22:17 +00:00
11eb74e44f
Request from Kiran: include PCT_TARGET_BASES_2X,PCT_TARGET_BASES_10X,
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PCT_TARGET_BASES_20X,PCT_TARGET_BASES_30X into pre-QC metrics.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5992 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 01:12:17 +00:00
1fec811a47
Updated input to accept BAM list, and output to emit proper sample name.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5991 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 00:15:01 +00:00
e0ed30681e
If data is not available, use R-compatible 'NA' string.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5987 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 18:53:38 +00:00
52f930d708
Bug fix.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5985 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 18:48:55 +00:00
1d1c9da783
First pass at a script that generates per-sample metrics from a pipeline yaml
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input file. Output is an R-parseable tsv.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5984 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 18:38:21 +00:00
fbb68ae94c
(Hopefully) short-lived script to rework the directory structure from core /
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playground / oneoffs to public / private. Currently implemented as an svn ->
svn merge, but will have to be tweaked to do a proper svn -> git merge.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5964 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-08 19:18:22 +00:00
d035d8eb7b
Updating the bam list is a bit trickier than most of us originally thought. Need to ensure that *3* files exist: the .bam, the .bai, and the finished.txt (or else bad things can happen)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5960 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-08 14:42:31 +00:00
8a0e813b04
A helper script that will take a list of bams, a list of case sample IDs, and a list of control sample IDs, and generate a sample meta data yaml (which includes the bamfiles)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5482 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-21 16:11:55 +00:00
4a09d25a90
One last little thing, I swear
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5423 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-11 17:37:40 +00:00
be1f6af815
Let's go the other way.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5422 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-11 17:36:41 +00:00
572b2707f2
oops
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5421 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-11 17:34:27 +00:00
aea0c733a4
A pilot for empirical recalibration of association scores.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5420 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-11 17:32:45 +00:00
b1b9c14c98
Minor utility improvements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5325 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-26 15:36:26 +00:00
44a48b4178
If you scatter depth of coverage and need to do something more sophisticated than gathering up (e.g. concatenating) the interval summary file, and need to smartly gather up a full summary file, modify (stress on MODIFY) this script to do it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5314 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-25 01:23:53 +00:00
a081f3b94f
Modifications, bugfix to theoretical posteriors. (Bug fix: eliminated discontinuity in prior distribution)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5239 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-14 19:47:34 +00:00
393df46055
updates to handle only reporting on a specific SVN revision. Updated the R script to show the domain name of the runner, now that S3 logging is working
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5157 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 12:02:12 +00:00
f8609afd4e
Committing two pieces of code for exome analysis, in case they need be returned to
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5135 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 14:13:09 +00:00
bccc71c481
updated to work with the new tearsheet
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5112 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 18:46:38 +00:00
32cdcc933c
A quick python script to give the status of the projects in the humgen/gsa-pipeline/ directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5070 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-25 15:21:50 +00:00
e64a300642
Deleting old python code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4961 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 21:33:45 +00:00
3362f0c280
Private mutation simulator and analysis routines for EOMI paper
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4960 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 21:23:29 +00:00
2448b859e4
no longer prints unnecessary table conversion failures that muck up emails. Run script now uses du not ls to display archive size
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4918 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-02 13:27:37 +00:00
501d44fa04
Minor bug fixee, replace double quotes with single quotes in strings so that R can read the resulting table
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4910 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-29 16:25:59 +00:00
46cd227613
Stabilitity improvements to GATK run report system. R code is now robust. XML parser uses the C backend in python, 10x faster. Added shell script that runs the daily reports, and linked the /humgen/ runme.csh to this script. Script now emails the group the daily PDFs to gsamembers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4845 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 14:56:12 +00:00
fabb42924c
Minor improvements to my crappy old python job management system. Mauricio's first task is to retire all of this code and move the DPP pipeline over to Queue
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4810 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-09 04:44:16 +00:00
984e94521e
Trival changes to data processing paper python
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4762 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 14:57:14 +00:00
187b464ded
calling pipeline for v13 of the paper calls -- the final version
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4716 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-22 21:57:12 +00:00
0e062ae040
V1 of the data processing paper, produced results for the manuscript we presented. Commit for archival purposes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4648 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 01:43:21 +00:00
fc39377e6c
Simple pre-processing script for soapsnp files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4627 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-04 20:34:43 +00:00
16c64558b4
Commenting out annoying print statement
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4566 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-24 11:55:26 +00:00
9fcfd8fa0d
analyzeRunReports now actually implements no-dev
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4557 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-22 19:53:23 +00:00
ccc22c2331
Adding a script to do big table conversion. Removing Ben's script which is totally obsolete and busted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4480 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-12 01:40:43 +00:00
04b4adafda
File reports are now sorted in order
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4447 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-06 21:54:23 +00:00
effcd26977
Shorter outputs, new summary mode
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4440 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-06 14:34:50 +00:00
cfebe5c731
clean-up the docs a little
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4375 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 05:02:41 +00:00
702449d835
adding a Python script to roll back tribble to the correct version, for users who want to checkout historical versions of the GATK code. This code cross references the current checkout date with the Tribble logs, and pulls the closest (price-is-right style) revision.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4374 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 05:01:46 +00:00
37613810bf
Tired of writing vcf_hg18_to_b36 over and over again when necessary. Added a -r flag to this script that does it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4363 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 14:51:57 +00:00
40274ba7dc
Do this the right way
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4310 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-19 04:30:48 +00:00
fa8cfd3031
Adding this to get around lsf/csh issues (see recent help message). Also seems like a good time to reiterate http://www.faqs.org/faqs/unix-faq/shell/csh-whynot/
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4309 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-19 02:45:16 +00:00
b57a0a0310
improvements to the report code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4280 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 00:45:13 +00:00
5de1124997
more useful reports
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4259 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:03:44 +00:00
droazen
kshakir
hanna
chartl
depristo
corin
ebanks
aaron