/vcf-filter

Java tool to filter an input VCF file a la carte, based on HTSJDK and Apache commons CLI.

Primary LanguageJavaMIT LicenseMIT

vcf-filter

Java tool to filter an input VCF file a la carte, based on HTSJDK and Apache commons CLI.

dependencies

Software Source
Java 1.8 https://www.java.com/es/download
picard.jar , included in lib/ https://github.com/broadinstitute/picard
commons-cli-1.3.1.jar, included in lib/ https://commons.apache.org/proper/commons-cli

compilation instructions

javac -cp lib/picard.jar:lib/commons-cli-1.3.1.jar:. Split.java VcfReader.java

check supported operations

If your system has Perl installed, as most Linux/Mac OS X systems, you can simply call:

./vcf-filter

Alternatively, just call it directly with java:

java -cp lib/picard.jar:lib/commons-cli-1.3.1.jar:. VcfReader

author

Eduardo Candeal, with help from Carlos P Cantalapiedra and Bruno Contreras-Moreira