Description and Quick Start
This is a workflow between Blat with psl output and SAM to BAM. There is a Blat step, then it uses script to convert psl files produced by BLAT into the SAM file format, and then the SAM file is converted to a BAM file.

Test Data
/iplant/home/shared/iplantcollaborative/example_data/Blat_with_BAM_output

Input File(s)
Input a fasta file, seqret.output

Output File(s)
A SAM file, and a BAM file.

References

https://genome.ucsc.edu/FAQ/FAQblat.html