I noticed that for one of the read pairs I am dealing with, bamclipper changes one of the reads to unmapped, while leaving the other read unchanged in terms of flags, so I get a broken pair (with the flag incorrectly saying that its mate is paired).
At the moment, I think I got around this issue by using fixmateinformation from Picard, but I was wondering whether there was an option in bamclipper to correct this internally
Thanks again!
(and it would be great if I can get the additional code for the clipping metrics for each pair!)
Hi Tommy,
I noticed that for one of the read pairs I am dealing with, bamclipper changes one of the reads to unmapped, while leaving the other read unchanged in terms of flags, so I get a broken pair (with the flag incorrectly saying that its mate is paired).
At the moment, I think I got around this issue by using fixmateinformation from Picard, but I was wondering whether there was an option in bamclipper to correct this internally
Thanks again! (and it would be great if I can get the additional code for the clipping metrics for each pair!)