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) 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)

AUTHOR

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