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runBWA Pipeline

runBWA Pipeline

Oct 27, 2014

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.