Home › User guide ›

Make paired file task

Submitted by editors on Wed, 06/09/2010 - 15:17

Make paired file task

Generates a paired end alignment file by using two sets of independently aligned left and right ends. 

Command:  java -Xmx2000m jar scripture.jar -task makePairedFile <Mandatory parameters> <Options> 
Mandatory Parameters

 -pair1: Path to one set of independently aligned left and right ends.  The alignment must be in SAM format and, ideally, should be sorted by read name. 

 -pair2: Path to the other set of independently aligned left and right ends.  The alignment must be in SAM format and, ideally, should be sorted by read name. 

 -out: Path to a file in which Scripture writes the paired end alignment file.  The output is an alignment in SAM format. 

Options

-sorted: This flag must be included if the two sets of independently aligned left and right ends are already sorted by read name.  Ideally, they should be.