focal (1) bammarkduplicatesopt.1.gz
NAME
bammarkduplicatesopt - mark duplicate reads/alignments in BAM files
SYNOPSIS
bammarkduplicatesopt [options]
DESCRIPTION
bammarkduplicatesopt reads a SAM/BAM/CRAM file containing alignments computed by an aligner, marks
duplicate reads/alignments using the coordinates of the alignments and writes the marked alignments to a
SAM/BAM or CRAM file. By default input is via standard input and output via standard output. Duplication
metrics are provided on the standard error channel by default. bammarkduplicatesopt scans the input BAM
file twice, it is thus of benefit to set the I key (described below) to give the name of an input file.
If the input BAM file is given via standard input, then a copy of the input will be stored in a temporary
file during the first run for processing in a second run. In contrast to bammarkduplicates this program
(bammarkduplicatesopt) specifically marks optical duplicates. Each optical duplicate read pair is marked
with an aux field stating which read in it's optical cluster is not considered to be an optical
duplicate.
The following key=value pairs can be given:
I=<stdin>: name of the input file (input is read from standard input if not set). This key can be given
multiple times. If it is given multiple times, then the input files need to be in coordinate sorted order
and will be merged for output such that the output will be coordinate sorted.
O=<stdout>: name of the output file (output is written to standard output if not set)
M=<stderr>: name of the metrics file (metrics are written to standard error if not set)
tmpfile=<filename>: prefix for temporary files. By default the temporary files are created in the current
directory
level=<-1|0|1|9|11>: set compression level of the output BAM file. Valid values are
-1: zlib/gzip default compression level
0: uncompressed
1: zlib/gzip level 1 (fast) compression
9: zlib/gzip level 9 (best) compression
If libmaus has been compiled with support for igzip (see https://software.intel.com/en-us/articles/igzip-
a-high-performance-deflate-compressor-with-optimizations-for-genomic-data) then an additional valid value
is
11: igzip compression
markthreads=<1>: Number of threads used during marking duplicate alignments.
verbose=<1>: Valid values are
1: print progress report on standard error
0: do not print progress report
mod=<1048576>: print progress after processing every mod'th input read/alignment (default is 1M)
rewritebam=<0|1|2>: compression type of the temporary file stored if I key is not given (input is via
standard input). Valid values are
0: temporary data is compressed using snappy (if available, see http://code.google.com/p/snappy/)
1: gzip/BAM, recompress input and store it as a BAM file
2: copy, produce a 1/1 copy of the input stream as a temporary file
rewritebamlevel=<-1|0|1|9|11>: compression level of temporary BAM file if rewritebam is 1 (see level key
for possible values).
colhashbits=<20>: base two logarithm of the size of the hash table used for collation (the default value
is 18 and should work reasonably well for most input files. Please see the biobambam paper at
arxiv.org/abs/1306.0836 for details).
collistsize=<33554432>: size of hash table overflow list in bytes (the default is 128MB and should work
reasonably well for most input files. Please see the biobambam paper at arxiv.org/abs/1306.0836 for
details).
fragbufsize=<50331648>: size of each fragment/pair file buffer in bytes (bammarkduplicatesopt uses two
such buffer for detecting duplicates)
rmdup=<0|1>: sets how duplicates are handled
0: duplicates will be retained in the output file and have the duplication flag set
1: duplicates will be remove when writing the output file
md5=<0|1>: md5 checksum creation for output file. Valid values are
0: do not compute checksum. This is the default.
1: compute checksum. If the md5filename key is set, then the checksum is written to the given file.
If the md5filename key is not given but set O key is set the checksum will be written as output
file name with .md5 appended. If md5filename and O are unset, then no checksum will be computed.
md5filename file name for md5 checksum if md5=1.
index=<0|1>: compute BAM index for output file. Valid values are
0: do not compute BAM index. This is the default.
1: compute BAM index. If the indexfilename key is set, then the BAM index is written to the given
file. If the indexfilename key is not given but set O key is set the checksum will be written as
output file name with .bai appended. If indexfilename and O are unset, then no BAM index will be
computed.
indexfilename file name for BAM index if index=1.
tag=<tag> name of auxiliary field storing tag information in string form. Read fragments or pairs with
different tags will not be considered as duplicates, even they would be according to their mapping
coordinates. For pairs the tag field information of the first and second mate are concatenated to obtain
the tag of the pair.
nucltag=<tag> this option works like the tag option but is restricted to sequences of nucleotides (A,C,G
or T) as tags. The length of each tag sequence is not allowed to exceed 15 bases. All tags are required
to have the same length. Each non nucleotide symbol is mapped to A. In constrast to the tag option,
nucltag uses less memory for processing and can be expected to be faster.
D ouptut file name for removed duplicates if rmdup=1. By default the reads and read pairs marked as
duplicates are discarded when rmdup=1. If the D key is set, then the sequence of reads which is not
written to the output file is written to a separate file. The name of this separate file is the value of
the D key.
dupmd5=<0|1>: compute md5 checksum of file given by D key if rmdup=1. By default no md5 checksum is
computed for this file.
dupmd5filename: file name for storing the md5 checksum of the D file if rmdup=1, D is set and dupmd5=1.
dupindex=<0|1>: compute BAM index for file given by D key if rmdup=1. By default no index is compute for
this file.
dupindexfilename: file name for storing the BAM index of the D file if rmdup=1, D is set and dupmd5=1.
optminpixeldif=<100>: distance (x and y inside same tile) inside which reads are considered as optical
duplicates
odtag=<od>: aux field tag for storing non dup read pair name for optical duplicates
addmatecigar=<0>: add mate cigar aux field MC and mate coordinate field mc
AUTHOR
Written by German Tischler.
REPORTING BUGS
Report bugs to <tischler@mpi-cbg.de>
COPYRIGHT
Copyright © 2009-2017 German Tischler, © 2011-2014 Genome Research Limited. License GPLv3+: GNU GPL
version 3 <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent
permitted by law.