conv_gtf_to_bed - legacy script for invoking the PALEOMIX command
[options] in.gtf out_prefix [in.scaffolds]
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
is a legacy script for invoking the paleomix(1) command
- Input file in GTF format.
- Prefix of output files.
- Mapping of scaffolds to contig positions; e.g. mapping
individual Un* scaffolds onto chrUn.
- -h, --help
- show this help message and exit
- Include all transcripts in the output BED files, not just
the longest transcript of each gene [default: off]
- 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
This manpage was written by Andreas Tille for the Debian distribution and can be
used for any other usage of the program.