NAME¶

bamreset - reset BAM file to unaligned state

SYNOPSIS¶

bamreset [options]

DESCRIPTION¶

bamreset reads a BAM file from standard input, transforms it to a pre aligned state and writes the resulting data to standard output as a BAM file.

Resetting the file involves the following actions:

Remove all SQ lines from the header.

Set the sorting order to unknown

Drop all non primary alignments

Remove all auxiliary fields

Mark all reads as unmapped and erase the mapping coordinates and template length fields

Move all reads to the forward direction by applying reverse complements as necessary such that afterwards no reverse complement flags are set.

The following key=value pairs can be given:

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

verbose=<1>: Valid values are

1:

print progress report on standard error

0:

do not print progress report

tmpfile=<filename>: prefix for temporary files. By default the temporary files are created in the current directory

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 md5filename is 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 indexfilename is unset, then no BAM index will be computed.

indexfilename file name for BAM index if index=1.

resetheadertext file name for replacement SAM header. By default the header of the input SAM/BAM/CRAM file is filtered.

exclude=<SECONDARY,SUPPLEMENTARY>: Do not include reads in the output that have any of the given flags set. The flags are given separated by commas. Valid flags are:

PAIRED:

read was paired in sequencing

PROPER_PAIR:

read has been mapped as part of a proper pair

UNMAP:

read was not mapped

MUNMAP:

mate of read was not mapped

REVERSE:

read was mapped to the reverse strand

MREVERSE:

mate of read was mapped to the reverse strand

READ1:

read was first read of a pair during sequencing

READ2:

read was second read of a pair during sequencing

SECONDARY:

alignment is secondary, i.e. an alternative mapping to the primary alignment in the same file

QCFAIL:

read as marked as having failed quality control

DUP:

read is marked as a duplicate of another read in the same file (see bammarkduplicates)

SUPPLEMENTARY:

read is marked as supplementary alignment

resetaux=<0|1>: auxiliary fields (default).

resetsortorder=<0|1>: set sort order to unknown if resetsortorder=1 (default) and leave as it is in the input if resetsortorder=0.

auxfilter=<>: comma separated list of aux tags to be kept if resetaux=0. If the key is not set when resetaux=0, then all tags are kept.

AUTHOR¶

Written by German Tischler.

REPORTING BUGS¶

Report bugs to <germant@miltenyibiotec.de>

COPYRIGHT¶

Copyright © 2009-2013 German Tischler, © 2011-2013 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.