Closed julia326 closed 6 years ago
Something like this:
0) split the initial aligned BAMs by chromosome 1) mark dups 2) split each by CIGAR string into one containing spliced reads and one not 3) run indel realigner on each chromosome's non-spliced-reads BAM 4) merge all the things
Something like this:
0) split the initial aligned BAMs by chromosome 1) mark dups 2) split each by CIGAR string into one containing spliced reads and one not 3) run indel realigner on each chromosome's non-spliced-reads BAM 4) merge all the things