runBWA Pipeline

runBWA.sh and runBWA_mem.sh pipelines are available on lonestar at:

/corral-repl/utexas/BioITeam/bin/runBWA.sh

/corral-repl/utexas/BioITeam/bin/runBWA_mem.sh

The pipelines do the following:

• Split data file into smaller chunks
• Run multiple, parallel BWA aln+sampe/mem instances 
• Concatenate results and provide that as the output.

Inputs:

• R1 fastq file

• R2 fastq file

• Prefix of BWA reference index (the absolute path)
• Number of chunks to split
• Output Directory
• TACC Allocation

Outputs:

• rs.cat.sam - mapping output in sam format

Run this pipeline on the head node. It will submit all jobs to the compute nodes.