Concatenante sorted VCF with same sample, does NOT merge genotypes
Usage: vcfconcat [options] Files
Options:
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --out
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 vcfconcat
The java jar file will be installed in the dist
directory.
The project is licensed under the MIT license.
Should you cite vcfconcat ? 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
$ find ./ -name "*.vcf" | grep Sample1 | java -jar dist/vcfconcat.jar > out.vcf
$ java -jar dist/vcfconcat.jar Sample1.samtools.vcf Sample1.gatk.vcf > out.vcf