Post date: May 12, 2014 3:27:14 PM
#We need to change the format from sam to bam, a compressed version of sam, and then we need to sort the bam files. See wrap_qsub_rc_sam2bam.pl. I changed "pbs.llucas" and the directory my sam files are in. On the USU cluster:
perl wrap_qsub_rc_sam2bam.pl alnE-BS-*sam
#Here's an example of the commands being submitted:
cd /labs/evolution/projects/sosorum/
samtools view -b -S -o alnE-BS-W-EL-034.bam alnE-BS-W-EL-034.sam
samtools sort alnE-BS-W-EL-034.bam alnE-BS-W-EL-034.sorted
samtools index alnE-BS-W-EL-034.sorted.bam
#Job #s: 253655-253912.torque. These should take about a day.