Post date: Sep 17, 2013 6:20:25 PM
I merged the four alignment files are re-sorted and indexed the bam alignments for the Timema whole-genome resequence data from plates 5 and 6 (primarily natural populations, including non cristinae). This was a bit tricky because the wrap_qsub script required passing a file glob to the bash script. I needed to remove the '-f' from the '#!/bin/bash -f' line in the perl script. The resulting sorted bam files are in data/timema/timema_wgrs/assemblies, begin with timema* and now have the population and individual gDNA individual ids. Next up, variant calling.