---
name: "maf-convert"
section: "1"
platform: "linux"
package: "last-align"
version: "1609-1+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/maf-convert"
---

# maf-convert(1)

Convert MAF-format alignments to tabular format

## NAME

maf-convert - Convert MAF-format alignments to tabular format

## DESCRIPTION

### Usage:

-

  maf-convert **--help** maf-convert axt mafFile(s) maf-convert bed mafFile(s) maf-convert blast mafFile(s) maf-convert blasttab mafFile(s) maf-convert blasttab+ mafFile(s) maf-convert chain mafFile(s) maf-convert gff mafFile(s) maf-convert html mafFile(s) maf-convert psl mafFile(s) maf-convert sam mafFile(s) maf-convert tab mafFile(s)

Read MAF-format alignments & write them in another format.

## OPTIONS

- **-h**, **--help**

  show this help message and exit

- **-s** N, **--subject**=*N*

  which sequence to use as subject/reference

- **-p**, **--protein**

  assume protein alignments, for psl match counts

- **-j** N, **--join**=*N*

  join consecutive co-linear alignments separated by \<= N letters

- **-J** N, **--Join**=*N*

  join nearest co-linear alignments separated by \<= N letters

- **-n**, **--noheader**

  omit any header lines from the output

- **-d**, **--dictionary**

  include dictionary of sequence lengths in sam format

- **-f** DICTFILE, **--dictfile**=*DICTFILE*

  get sequence dictionary from DICTFILE

- **-r** READGROUP, **--readgroup**=*READGROUP*

  read group info for sam format

- **-l** LINESIZE, **--linesize**=*LINESIZE*

  line length for blast and html formats (default: 60)