Set the ##contig
lines in a VCF header on the fly
Usage: vcfsetdict [options] Files
Options:
--bcf-output
If this program writes a VCF to a file, The format is first guessed from
the file suffix. Otherwise, force BCF output. The current supported BCF
version is : 2.1 which is not compatible with bcftools/htslib (last
checked 2019-11-15)
Default: false
--generate-vcf-md5
Generate MD5 checksum for VCF output.
Default: false
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-n, --onNotFound
Contig converter. I will do my best to convert the contig names (e.g
'chr1' -> '1'): But what should I do when comparing two dictionaries
with different notations
Default: SKIP
Possible Values: [RAISE_EXCEPTION, SKIP, RETURN_ORIGINAL]
-o, --out
Output file. Optional . Default: stdout
* -r, -R, --reference
Indexed fasta Reference file. This file must be indexed with samtools
faidx and with picard CreateSequenceDictionary
--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 vcfsetdict
The java jar file will be installed in the dist
directory.
20140105
The project is licensed under the MIT license.
Should you cite vcfsetdict ? 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
The tool will try to convert the contig names (β1β -> βchr1β) according to the new dictionary.
java -jar jvarkit-git/vcfsetdict.jar --onNotFound SKIP -r ref.fasta input.vcf > out.vcf