User contributions
19 April 2019
BamUtil: recab
Required Generic Parameters
+10
BamUtil: recab
Handling Recalibration/Implementation Notes
+31
8 April 2019
BamUtil: dedup
Required Parameters
+10
Template:InBAMInputFile
no edit summary
+6
Template:InBAMInputFile
no edit summary
+1
Template:InBAMInputFile
no edit summary
+42
Template:InBAMInputFile
no edit summary
+26
Template:InBAMInputFile
no edit summary
+120
BamUtil: dedup
Overview of the dedup function of bamUtil
+72
BamUtil: dedup
Implementation Notes
+76
30 July 2018
13 November 2017
LibStatGen Troubleshooting
Possible Compile Errors
+264
Template:ToolGitRepo
no edit summary
+273
LibStatGen Download
Official Releases
+913
12 November 2017
BamUtil
Full Release (includes libStatGen)
+235
BamUtil
Release of just BamUtil (does not include libStatGen)
+762
BamUtil: trimBam
Soft Clipping Notes (--clip/-c)
+13
BamUtil: trimBam
Soft Clipping Notes (--clip/-c)
+26
9 September 2017
24 August 2017
BamUtil: stats
BaseQC (--pBaseQC and --cBaseQC and --baseSum)
+11
BamUtil: stats
BaseQC (--pBaseQC and --cBaseQC and --baseSum)
+29
BamUtil: stats
Parameters
+479
14 June 2017
4 January 2017
14 April 2016
6 March 2016
BamUtil: gapInfo
Rules
+26
BamUtil: recab
Parameters
+1,246
BamUtil: recab
Skip Records with any of the Specified Flags (--buildExcludeFlags, --applyExcludeFlags)
-22
BamUtil: dedup
Skip Records with any of the Specified Flags (--excludeFlags)
-109
BamUtil: dedup
Skip Records with any of the Specified Flags (--excludeFlags)
+143
BamUtil: dedup
Parameters
+43
BamUtil: clipOverlap
ASSUMPTIONS/RESTRICTIONS
+95
BamUtil: clipOverlap
Parameters
5 March 2016
BamUtil: clipOverlap
Skip Records with any of the Specified Flags (--excludeFlags)
-29
BamUtil: bam2FastQ
Parameters
+1,936
BamUtil: bam2FastQ
Usage
+102
BamUtil: bam2FastQ
Overview of the bam2FastQ function of bamUtil
-100
28 January 2016
28 October 2015
19 August 2015
30 June 2015
GotCloud: Creating a New Pipeline
Example Pipelines Created
+78
GotCloud: Creating a New Pipeline
Overall Pipeline Definition
+163
GotCloud: Creating a New Pipeline
Defining a New Pipeline
GotCloud: Creating a New Pipeline
no edit summary
+2,508
GotCloud: Creating a New Pipeline
Configure Each Step
+3,041
GotCloud: Creating a New Pipeline
Defining a New Pipeline
+1,180
