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> 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.
Am I missing something. I can also share history  in order to explain my
point if required.

Thanks

Kanwar
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