Post date: Sep 16, 2013 6:51:9 PM
I compressed, sorted, and indexed the 764 individual sam alignments for the whole genome resequence data from plates 5 and 6. This was accomplished with the samtools commands view, sort, and index which were run with wrap_qsub_rc_sam2bam.pl in data/timema/timema_wgrs/assemblies/. Next I will need to merge these alignments by individual (four alignments currently exist for each alignment).