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- 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
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Outputs:
- rs.cat.sam - mapping output in sam format
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Run this pipeline on the head node. It will submit all jobs to the compute nodes.
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