I have a sam file after running BWASW and want to extract unique (alignments that are aligning once to genome) from this sam file. I read in other posts that I may be able to use Sam tools&gt; filter Sam option to filter the said flag on wise flag. However I could not find whether I have to use default setting of column 2? when I use option of add flags there are different options for pair reads, however my data is single reads. So exactly single read alignments sam file how we extract unique reads.<div>

Am I missing something. I can also share history  in order to explain my point if required.</div><div><br></div><div>Thanks</div><div><br></div><div>Kanwar<br><div><br></div><div> </div></div>