---
name: "wham"
section: "1"
platform: "linux"
package: "wham-align"
version: "0.1.5-8"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/wham"
---

# wham(1)

Wisconsin's High-Throughput Alignment Method

## 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.