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.