1> I have been using MAQ for a while. Now I would like to move on the BWA. Is there any convinent method to convert a MAQ output (.map) to SAM format so to ease comparison between MAQ and BWA?
2> Regarding the SAM format output by BWA, there is a <flag> column. I read from the manual that it's a bitwise flag. But in my BWA output I get numeric value, (e.g. 83, 99, 163, etc). How can I interpret the result?
I would really appreciate your help.
2> Regarding the SAM format output by BWA, there is a <flag> column. I read from the manual that it's a bitwise flag. But in my BWA output I get numeric value, (e.g. 83, 99, 163, etc). How can I interpret the result?
I would really appreciate your help.
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