bammarkduplicatesopt - mark duplicate reads/alignments in BAM files
bammarkduplicatesopt [options]
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 removed 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 contrast
to the tag option, nucltag uses less memory for processing and can be expected
to be faster.
D output 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
Written by German Tischler.
Report bugs to <
[email protected]>
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.