Post date: May 02, 2017 4:0:17 AM
1v17. The assemblies finished, and we started 614 more. All finished by the end of the day. Then:
We compressed (converted to bam), sorted and indexed the alignment
files. The files are in
/uufs/chpc.utah.edu/common/home/u6000989/data/lycaeides/lycaeides_gbs/AssembliesGwa/.
From that directory I ran,
perl ../Scripts/wrap_qsub_slurm_sam2bam.pl *sam
Here is the set of commands for one sample (as an example):
cd
/uufs/chpc.utah.edu/common/home/u6000989/data/lycaeides/lycaeides_gbs/AssembliesGwa/
samtools view -b -S -o alnYWP12-39M.bam alnYWP12-39M.sam
samtools sort alnYWP12-39M.bam alnYWP12-39M.sorted
samtools index alnYWP12-39M.sorted.bam
We did this for 869 files total (the others were already run for other
projects).