USeq / Source Code Commit Log

Commit	Date
[r177] by tmosbruger VCFAnnotator: This app now supports VAAST 2.0 output, including InDels	2013-11-06 21:51:37	Tree
[r176] by biotelerock SRAProcessor * Added option to set quality score offset to 64, needed for some Illumina datasets MiRNACorrelator * Added ggplot2 box whisker plot functionality	2013-11-06 21:17:25	Tree
[r175] by tmosbruger TomatoFarmer: Implement deleteing intermediate bams TFCommandExomeVariant: Fixed chunking behavior when inverval exactly matches remaining chunk space. This produced a zero length interval, which GATK dislikes.	2013-11-06 15:45:06	Tree
[r174] by biotelerock Updated docs for chIPSeq and RNASeq.	2013-11-04 23:47:24	Tree
[r173] by tmosbruger MultiSampleVCFFilter: Allow strict genotype matching, which drops records with missing genotypes.	2013-11-04 20:36:50	Tree
[r172] by biotelerock DefinedRegionDifferentialSeq * Added a System.setProperty("java.awt.headless", "true") to allow running app in non x11 mode. VCFSample * Changed how it recognizes a no call to anything that starts with ./. so these are skipped FilterIntersectingRegions * Added option to split gtf/ gff files	2013-11-04 20:32:34	Tree
[r171] by tmosbruger Added support for BWA mem. This broke some of the USeq apps that expect a single alignment per pair and didn't check the primary flag. Remove hard-coded paths to software and added them to the config file. I don't like a user-specified config file... I need to come up with a better solution Changed the names of the output VCF files, 'filtered' and 'passing' was too cryptic. Files are now 'filterFieldSetAll' and 'filterFieldSetPassing', much clearer? Merged 'primary' and 'padded' target bed file and added AgilentV5UTR to list.	2013-11-04 00:18:57	Tree
[r170] by tmosbruger GATK and Annovar format InDels differently. InDels were labeled 'substitutions', now they are properly labeled insertions and deletions.	2013-11-03 03:01:08	Tree
[r169] by tmosbruger TomatoFarmer Update	2013-11-02 00:06:08	Tree
[r168] by monkeymanstan 1. Fixed soft-linking of 101bp paired-end RNA-Seq data 2. Added updated alignments params for 101bp paired-end RNA-Seq data 3. Updated sequencing application codes to include new applications and removed outdated ones 4. Updated miRNA alignment params 5. Removed code to make the QC, processedAlignments, and coverageTracks dirs in GNomEx, as it appears that most users delete them and make their own 6. Changed dir path of tomato/job/ to /tomato/dev/job/ to work with Tomato3 7. Changed path of autoalignerData to /tomato/dev/job/autoaligner/autoalignerData/ 8. Changed path of apps to /tomato/dev/job/autoaligner/apps/ 9. Changed the number of lines in each split bisulfite fastq file to cut down on file #	2013-10-24 13:54:44	Tree

[r177] by tmosbruger

VCFAnnotator: This app now supports VAAST 2.0 output, including InDels

2013-11-06 21:51:37

[r176] by biotelerock

SRAProcessor
* Added option to set quality score offset to 64, needed for some Illumina datasets
MiRNACorrelator
* Added ggplot2 box whisker plot functionality

2013-11-06 21:17:25

Tree

[r175] by tmosbruger

TomatoFarmer: Implement deleteing intermediate bams
TFCommandExomeVariant: Fixed chunking behavior when inverval exactly matches remaining chunk space. This produced a zero length interval, which GATK dislikes.

2013-11-06 15:45:06

Tree

[r174] by biotelerock

Updated docs for chIPSeq and RNASeq.

2013-11-04 23:47:24

Tree

[r173] by tmosbruger

MultiSampleVCFFilter: Allow strict genotype matching, which drops records with missing genotypes.

2013-11-04 20:36:50

Tree

[r172] by biotelerock

DefinedRegionDifferentialSeq
* Added a System.setProperty("java.awt.headless", "true") to allow running app in non x11 mode.

VCFSample
* Changed how it recognizes a no call to anything that starts with ./. so these are skipped

FilterIntersectingRegions
* Added option to split gtf/ gff files

2013-11-04 20:32:34

Tree

[r171] by tmosbruger

*Added support for BWA mem. This broke some of the USeq apps that expect a single alignment per pair and didn't check the primary flag.
*Remove hard-coded paths to software and added them to the config file. I don't like a user-specified config file... I need to come up with a better solution
*Changed the names of the output VCF files, 'filtered' and 'passing' was too cryptic. Files are now 'filterFieldSetAll' and 'filterFieldSetPassing', much clearer?
*Merged 'primary' and 'padded' target bed file and added AgilentV5UTR to list.

2013-11-04 00:18:57

Tree

[r170] by tmosbruger

GATK and Annovar format InDels differently. InDels were labeled 'substitutions', now they are properly labeled insertions and deletions.

2013-11-03 03:01:08

Tree

[r169] by tmosbruger

TomatoFarmer Update

2013-11-02 00:06:08

Tree

[r168] by monkeymanstan

1. Fixed soft-linking of 101bp paired-end RNA-Seq data
2. Added updated alignments params for 101bp paired-end RNA-Seq data
3. Updated sequencing application codes to include new applications and removed outdated ones
4. Updated miRNA alignment params
5. Removed code to make the QC, processedAlignments, and coverageTracks dirs in GNomEx, as it appears that most users delete them and make their own
6. Changed dir path of tomato/job/ to /tomato/dev/job/ to work with Tomato3
7. Changed path of autoalignerData to /tomato/dev/job/autoaligner/autoalignerData/
8. Changed path of apps to /tomato/dev/job/autoaligner/apps/
9. Changed the number of lines in each split bisulfite fastq file to cut down on file #

2013-10-24 13:54:44

Tree

USeq Source Code

Source Code Commit Log