7d2df3f511
example windowed ROD walker for Kristian, and updates to Tribble
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3325 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 17:12:50 +00:00
57f254b13a
VE integration test
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3324 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 13:58:25 +00:00
7cab994d88
Add argument to sortByRef for specifying the tmp directory for sorting.
...
Update the liftover script to reflect this addition.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3323 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 13:53:26 +00:00
bfc58c70fa
Adding newline
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3322 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 13:08:08 +00:00
44de92e09d
Checking in the liftover script. I am including a post-processing walker to filter out bad records written in under 10 minutes as per my agreement with Mark.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3321 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 12:31:56 +00:00
18f1d31a22
Moving to and organizing in core.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3320 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 04:05:36 +00:00
06ea65e60b
again for JIRA GSA-320
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3319 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 03:47:58 +00:00
ac9b32db88
a bug fix for Kiran; putting JIRA in for better type determination system for the new Tribble tracks so this doesn't happen again.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3318 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 03:31:43 +00:00
4e0019b04f
Repair code that sorts and merges intervals.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3317 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 22:37:25 +00:00
72e030a670
require that snps be biallelic before we pass them to the TiTv calculation.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3316 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 22:33:00 +00:00
3b52ac67e0
adding the Tribble codecs to the package.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3315 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 21:06:15 +00:00
7cecec7d00
Removing zero no-calls restriction in AC stats
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3314 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 18:55:07 +00:00
0e58fb7cc0
Moved over to be a walker inside the GATK
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3313 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 18:28:03 +00:00
78409dca0d
turned off the progress output from tribble when making an index, and fixing a case where the index file isn't writable so we instead make the index in memory.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3312 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 16:36:58 +00:00
bacc507a48
Don't worry about sorting anymore in the liftover tool. That will come later.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3311 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 15:00:30 +00:00
d91b27aca1
updating Tribble with VCF changes from Eric
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3310 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 04:03:21 +00:00
5df0361bd2
trivial removal of unnecessary comments
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3309 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 03:51:14 +00:00
2975e3a4e8
picard Intervals don't sort right - switching to GenomeLocs
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3308 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 03:50:28 +00:00
7467ec2fd6
updating the reflections library; Matt found a problem where the reflections library doesn't sort out non-java objects from the classpath (affects only OS X so far). I'll push back the changes to
...
the reflections library people.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3307 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-06 02:08:41 +00:00
1a99fb9318
First pass at liftover tool. Passing buck over to Aaron...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3306 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 20:38:19 +00:00
a0d71540df
speed-up for VCF, adding code to the VCF reader to automagically make an index if one doesn't already exist, and a change to the VCF writer unit test
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3305 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 20:19:42 +00:00
6bbcc47b5d
removing some out-of-date RODs and some unused genotype writer formats
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3304 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 19:07:13 +00:00
c998c48a23
adding code to detect out-of-date index files, which we now remove and regenerate if the target file is newer than the index file.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3303 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 17:55:36 +00:00
a68f3b2e9c
VCF moved over to tribble.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3302 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 17:28:48 +00:00
ad11201235
adding more ROD pile-up tests
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3301 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 16:01:11 +00:00
0338345bee
Fixing the issue with reads having insertion immediately followed by a S/H cigar element causing out of window error.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3300 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 15:42:27 +00:00
64640d6b17
Complete the switch statement to deal with all possible cigar operators for Kris.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3299 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 13:41:05 +00:00
f75e54e3f7
fixes for new package names in tribble 74
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3298 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 05:47:04 +00:00
97dd04cbf0
updating Tribble ahead of the big VCF commit
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3297 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 05:17:54 +00:00
617542853f
Walker that can be used with refGene and a TCGA bed file to annotate intervals in an interval list with the genes and exons they overlap.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3296 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 02:55:01 +00:00
354262eabe
New convenience methods to rodRefSeq for dealing with intervals that may be a superset of multiple exons. Needed for next commit.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3295 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 02:54:18 +00:00
d5b675b3e6
Added - Q&D script to gather verbose bed files to a VCF.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3294 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 02:49:16 +00:00
03bea70f3a
Fixed edge case bug in cleaner: when no -L argument is used and a target interval abuts the end of the reference genome, we'll NullPointer at the first unmapped read.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3293 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-04 16:49:21 +00:00
510b3efcc2
Fixed an issue where asking for the alternate alleles at hom-ref sites would result in an array out-of-bounds exception.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3292 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 18:46:33 +00:00
a462b5e1e7
Changed a default path
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3291 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 17:07:21 +00:00
94b51de401
HLA caller updated to examine class II loci, updated pointers to dictionary, allele frequencies.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3290 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 14:54:52 +00:00
97fdd92e7b
Clean up the code to have a unified approach to calculating p(true) for both with and without ti/tv models
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3289 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 13:30:20 +00:00
f497213933
DbSNP moved over to tribble
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3288 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 06:02:35 +00:00
447081583a
rev tribble with updated version
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3287 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 04:07:28 +00:00
9d01670f62
Major update to the Variant Optimizer. It now performs clustering for both the titv and titv-less models simultaneously, outputting the cluster files at every iteration. It makes use of the Jama matrix library to do full inverse and determinant calculation for the covariance matrix where before it was using only approximations.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3286 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-02 19:21:23 +00:00
a318b1871d
Removed unused column
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3285 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 21:29:34 +00:00
9dff578706
Added PG tag to bam header to let people know it's been cleaned.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3284 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 17:30:30 +00:00
28f746b76a
Added option to generate UCSC or NCBI sequence
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3283 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 17:26:00 +00:00
0e10359a5e
Okay, finished up the ability to cap a base's qual by its read's mapping quality.
...
This is experimental - I have not tested its performance on SNP calling, or even played around with it. If you want to test it out, go nuts. But don't come running to me if your results are not good.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3282 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 16:58:30 +00:00
850f36aa61
Changes to the Unified Genotyper's arguments:
...
1. User can specify 4 confidence thresholds: for calling vs. emitting and at standard vs. 'trigger' sites.
2. User can cap the base quality by the read's mapping quality (not done yet).
3. Default confidence threshold is now Q30.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3281 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 16:44:24 +00:00
8b2ce128b5
Optimized the join(..) method.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3280 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:55:07 +00:00
c214056d88
Script for concatenating results of GenerateTranscriptToInfo.py into one big file
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3279 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:47:08 +00:00
8bb15ef812
Checking in the reference implementation of the downsampler for back comparison.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3278 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:41:13 +00:00
0069cb426d
Script for spawning LSF jobs that run the TranscriptToInfo.java walker on each of the 50 contigs.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3277 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:27:52 +00:00
ba7fe7c4e1
Renamed
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3276 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:25:07 +00:00
aaron
rpoplin
ebanks
hanna
asivache
chartl
kiran
weisburd
sjia