bam_rmdup_collapsed - filter BAM file for PCR duplicates

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

bam_rmdup_collapsed 1.2.7                         February 2017                           BAM_RMDUP_COLLAPSED(1)

       The  rmdup_collapsed  filters  a BAM file for PCR duplicates unpaired reads under the assumption that any
       unpaired read have been generated by the merging of overlapping paired-end reads, and  thereby  represent
       the  complete  template  sequence.  PCR  duplicates  are  therefore  detected based on both the 5' and 3'
       alignment coordinate.

       Paired reads (0x1), unmapped reads (0x4), secondary alignments (0x100), reads that failed QC (0x200), and
       chimeric alignments (0x800), as identified using the BAM record  flags,  are  not  filtered,  but  simply
       written to the output.

       By default, filtered reads are flagged using the "duplicate" flag (0x400), and written to the output. Use
       the --remove-duplicates command-line option to instead remove these records from the output.

       This program is part of the paleomix(1) suite.

       bam_rmdup_collapsed - filter BAM file for PCR duplicates

positionalarguments:
       input  BAM file; if not set, input is read from STDIN.

   optionalarguments:-h, --help
              show this help message and exit

       --remove-duplicates
              Remove duplicates from output; by default duplicates are only flagged (flag = 0x400).

       --seed SEED
              Seed  used  for  randomly  selecting  representative  reads  when  no  reads  have  quality scores
              assigned[default: initialized using system time].

paleomix(1)

paleomixrmdup_collapsed [options] < sorted.bam > out.bam