wham(1)

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