Post date: Jan 06, 2014 11:12:30 PM
I used samtools to compress (covert to bam), sort and index the sequence data for the sv detection. The results are in /home/A01963476/data/timema/timema_sv and an example of the command I used is:
cd /home/A01963476/data/timema/timema_sv/
samtools view -b -S -o R23A-ART005.bam R23A-ART005.sam
samtools sort R23A-ART005.bam R23A-ART005.sorted
samtools index R23A-ART005.sorted.bam
I might still want to remove low quality alignments, but otherwise the bam files are ready for Philine