.TH CONV_GTF_TO_BED "1" "February 2017" "conv_gtf_to_bed 1.2.7" "User Commands"
.SH NAME
conv_gtf_to_bed \- legacy script for invoking the PALEOMIX command "gtf_to_bed"
.SH SYNOPSIS
.B paleomix gtf_to_bed
[options] in.gtf out_prefix [in.scaffolds]
.SH 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.
.P
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.
.P
\fBconv_gtf_to_bed\fR is a legacy script for invoking the paleomix(1) command "gtf_to_bed"
.SH OPTIONS
.SS "positional arguments:"
.TP
INPUT.gtf
Input file in GTF format.
.TP
OUTPUT_PREFIX
Prefix of output files.
.TP
SCAFFOLDS
Mapping of scaffolds to contig positions; e.g. mapping
individual Un* scaffolds onto chrUn.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-keep\-all\-transcripts\fR
Include all transcripts in the output BED files, not
just the longest transcript of each gene [default:
off]
.TP
\fB\-\-keep\-malformed\-proteins\fR
Include transcripts of protein\-coding in the output,
even if the the length of the CDS is not divisible by
3 [default: off]
.TP
\fB\-\-contig\-prefix\fR CONTIG_PREFIX
Add prefix to contig names (e.g. 'chr') [default: no
prefix].
.SH SEE ALSO
paleomix(1)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.