Post date: Jan 08, 2014 11:32:22 PM
I am using the bit fields and alignment qualities to filter the SV alignments. This will only retain reads with alignment qualities of 40 or more and where both read pairs are properly mapped. Here is an example:
cd /home/A01963476/data/timema/timema_sv/
samtools view -b -h -q 40 -F 4 -F 8 -f 1 -f 2 R23A-ART005.sorted.bam > R23A-ART005.filtered.bam