Post date: Jan 23, 2015 6:20:23 PM
The alignments appear to have went well. The one I checked had about 50% of the sequences align with 40% to genome scaffolds and 10% to GBS contigs. So, I am not compressing, sorting and indexing all 576 alignments (and cleaning up along the way):
cd /labs/evolution/data/callosobruchus/gbs/Assemblies/gbs2ref/
samtools view -b -S -o alnM-14-48.bam alnM-14-48.sam
rm alnM-14-48.sam
samtools sort alnM-14-48.bam alnM-14-48.sorted
rm alnM-14-48.bam
samtools index alnM-14-48.sorted.bam