---
name: "conv_gtf_to_bed"
section: "1"
platform: "linux"
package: "paleomix"
version: "1.3.8-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/conv_gtf_to_bed"
---

# conv\_gtf\_to\_bed(1)

legacy script for invoking the PALEOMIX command "gtf\_to\_bed"

## NAME

conv\_gtf\_to\_bed - legacy script for invoking the PALEOMIX command "gtf\_to\_bed"

## SYNOPSIS

**paleomix gtf\_to\_bed** \[options\] in.gtf out\_prefix \[in.scaffolds\]

## DESCRIPTION

The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data: The BAM pipeline processes de-multiplexed reads from one or more samples, through sequence processing and alignment, to generate BAM alignment files useful in downstream analyses; the Phylogenetic pipeline carries out genotyping and phylogenetic inference on BAM alignment files, either produced using the BAM pipeline or generated elsewhere; and the Zonkey pipeline carries out a suite of analyses on low coverage equine alignments, in order to detect the presence of F1-hybrids in archaeological assemblages. In addition, PALEOMIX aids in metagenomic analysis of the extracts.

The pipelines have been designed with ancient DNA (aDNA) in mind, and includes several features especially useful for the analyses of ancient samples, but can all be for the processing of modern samples, in order to ensure consistent data processing.

**conv\_gtf\_to\_bed** is a legacy script for invoking the [paleomix(1)](/paleomix/1.md) command "gtf\_to\_bed"

## OPTIONS

### positional arguments:

- INPUT.gtf

  Input file in GTF format.

- OUTPUT\_PREFIX

  Prefix of output files.

- SCAFFOLDS

  Mapping of scaffolds to contig positions; e.g. mapping individual Un\* scaffolds onto chrUn.

### optional arguments:

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

  show this help message and exit

- **--keep-all-transcripts**

  Include all transcripts in the output BED files, not just the longest transcript of each gene \[default: off\]

- **--keep-malformed-proteins**

  Include transcripts of protein-coding in the output, even if the the length of the CDS is not divisible by 3 \[default: off\]

- **--contig-prefix** CONTIG\_PREFIX

  Add prefix to contig names (e.g. 'chr') \[default: no prefix\].

## SEE ALSO

[paleomix(1)](/paleomix/1.md)

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.