Scan retrocopies by comparing the gtf/intron and the deletions in a VCF
Usage: gtfretrocopy [options] Files
Options:
--all
all introns must be found
Default: false
-d, --distance
max distance between an intron and the deletion found in the VCF
Default: 10
--generate-vcf-md5
Generate MD5 checksum for VCF output.
Default: false
* -gtf, --gtf
A GTF (General Transfer Format) file. See
https://www.ensembl.org/info/website/upload/gff.html .
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
--id, -id
Which key should I use for the column ID. The idea is to use the gene
name to get the uniq entities per vcf.
Default: transcript_id
Possible Values: [transcript_id, gene_id, gene_name]
-k, --known
Gene-ID of known retrogenes. One per line. A source could be :
http://retrogenedb.amu.edu.pl/static/download/
-o, --output
Output file. Optional . Default: stdout
--version
print version and exit
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew gtfretrocopy
The java jar file will be installed in the dist
directory.
20190813
The project is licensed under the MIT license.
Should you cite gtfretrocopy ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
java -jar dist/gtfretrocopy.jar --gtf transcript.gtf.gz input.vcf.gz > retrocopies.vcf