NAME

       bam_rmdup_collapsed - filter BAM file for PCR duplicates

SYNOPSIS

       paleomix rmdup_collapsed [options] < sorted.bam > out.bam

DESCRIPTION

       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.

OPTIONS

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

   optional arguments:
       -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].

SEE ALSO

       paleomix(1)

AUTHOR

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