bamclipXT1

Usage

Overview

bamclipXT processes a SAM/BAM/CRAM file containing the XT flag produced by Picard's MarkIlluminaAdapters and sets the designated base qualities to 2. The original base qualities are copied to a new aux tag named cq (clipped quality). The resulting data is then written as a SAM/BAM/CRAM file.

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

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.