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VCFBigWig
annotates a VCF file with a bigwig file Download and Compilesvn checkout http://jvarkit.googlecode.com/svn/trunk/ jvarkit cd jvarkit edit the file build.properies and add the path to the picard and bigwi API ( http://code.google.com/p/bigwig/) picard.jar=/path/to/picard-tools-1.79/picard-1.79.jar sam.jar=/path/to/picard-tools-1.79/sam-1.79.jar bigwig.dir=/path/to/packages/bigwig.directory and compile: ant vcfbigwig Usagejava -jar dist/vcfbigwig.jar -f file.bw (file.vcf|stdin) Options-f (bigwig-file) required. -i (String) VCF-ID optional. Example$ java -jar dist/vcfbigwig.jar -f /commun/data/pubdb/ucsc/hg19/bbi/All_hg19_RS_noprefix.bw test.vep.vcf ##fileformat=VCFv4.1 ##Annotated with class fr.inserm.umr1087.jvarkit.tools.vcfbigwig.VCFBigWig:/commun/data/pubdb/ucsc/hg19/bbi/All_hg19_RS_noprefix.bw ##INFO=<ID=All_hg19_RS_noprefix,Number=1,Type=Float,Description="Annotations from /commun/data/pubdb/ucsc/hg19/bbi/All_hg19_RS_noprefix.bw"> #CHROM POS ID REF ALT QUAL FILTER INFO 22 12345 . G T 100.0 . All_hg19_RS_noprefix=4.829999923706055 |