Hey all,
I want to take an aligned file, run it through Dindel, output realigned windows, and merge the realigned windows with the original aligned file. If I ran the entire aligned file through Dindel I could just use the realigned windows and be done. However, to save time, I'd rather just have Dindel look at candidate windows. Thus, only a subset of reads in the aligned file will be pulled to be run through Dindel.
Another way to state this, I want to take a subset of reads in an aligned file, alter them, and replace the original versions with the altered versions. Is there an easy way to do this? Thanks!
I want to take an aligned file, run it through Dindel, output realigned windows, and merge the realigned windows with the original aligned file. If I ran the entire aligned file through Dindel I could just use the realigned windows and be done. However, to save time, I'd rather just have Dindel look at candidate windows. Thus, only a subset of reads in the aligned file will be pulled to be run through Dindel.
Another way to state this, I want to take a subset of reads in an aligned file, alter them, and replace the original versions with the altered versions. Is there an easy way to do this? Thanks!
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