---
name: "gt-chseqids"
section: "1"
platform: "linux"
package: "genometools"
version: "1.6.5+ds-2.2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gt-chseqids"
---

# gt-chseqids(1)

Change sequence ids by the mapping given in a mapping file.

## NAME

gt-chseqids - Change sequence ids by the mapping given in a mapping file.

## SYNOPSIS

**gt chseqids** \[option ...\] mapping\_file \[GFF3\_file\]

## DESCRIPTION

- **-sort** \[*yes\|no*\]

  sort the GFF3 features after changing the sequence ids (memory consumption is proportional to the input file size) (default: no)

- **-v** \[*yes\|no*\]

  be verbose (default: no)

- **-o** \[*filename*\]

  redirect output to specified file (default: undefined)

- **-gzip** \[*yes\|no*\]

  write gzip compressed output file (default: no)

- **-bzip2** \[*yes\|no*\]

  write bzip2 compressed output file (default: no)

- **-force** \[*yes\|no*\]

  force writing to output file (default: no)

- **-help**

  display help and exit

- **-version**

  display version information and exit

File format for mapping\_file:

The supplied mapping file defines a mapping table named “chseqids”. It maps the sequence-region entries given in the GFF3\_file to other names. It can be defined as follows:

```
chseqids = {
  chr1  = "seq1",
  chr2  = "seq2"
}
```

When this example is used, all sequence ids “chr1” will be changed to “seq1” and all sequence ids “chr2” to “seq2”.

## REPORTING BUGS

Report bugs to https://github.com/genometools/genometools/issues.