Man page - wham(1)
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Manual
WHAM
NAMEDESCRIPTION
Usage:
Input options:
Alignment options:
Reporting options:
Output options:
Performance options:
Other options:
AUTHOR
NAME
wham - Wisconsin’s High-Throughput Alignment Method
DESCRIPTION
Usage:
wham [options]* {<readfile> | -1 <m1file> -2 <m2file>} <basepath> <output> <readfile> comma-separated list of files containing unpaired reads <m1file> comma-separated list of files containing upstream mates <m2file> comma-separated list of files containing downstream mates <basepath> write wham data to files with this dir/basename <output> file to write alignments to
Input options:
-l <int>
use first <int> bases in each read
Alignment options:
-v <int>
specify the max number of errors in a reported alignment.
-g /--gap <int>
specify the max number of gaps in a reported alignment.
-e /--maqerr <int>
max sum of mismatch quals across alignment
--nofw /--norc
do not align to forward/reverse-complement ref strand
--nofr /--norf
do not align to mate1/mate2 strand: fw/rev, rev/fw.
-I /--minins <int>
minimum insert size for paired-end alignment (default: 0).
-X /--maxins <int>
maximum insert size for paired-end alignment (default: 250).
Reporting options:
-k <int>
report up to <int> valid alignemtns per read (default: 1).
-a /--all
report all valid alignments per read.
|
--best |
reprot valid alignments in a sorted order of quality. |
-m <int>
discard reads with more than <int> valid alignmetns.
Output options:
-S /--sam
write alignment in SAM format
--al <fname>
write aligned reads/pairs to file(s) <fname>
--un <fname>
write unaligned reads/pairs to file(s) <fname>
Performance options:
-t <int>
specify the number of threads
--nocat
do not concatenate results from various threads
--step <int>
specify the number of indexes that fit into memory.
Other options:
--version
print version information
-h /--help
print this usage message
AUTHOR
This manpage was
written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.