j5kim/vcfannotationwithsnpeff repository overview

⁠download the example input data

wget -O - ftp://gsapubftp-[email protected]⁠/bundle/2.8/hg19/NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.vcf.gz |
gunzip -c > NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.vcf

⁠run snpEff

java -Xmx8g -jar /opt/bin/snpEff/snpEff.jar -v GRCh37.75 -c /opt/bin/snpEff/snpEff.config
NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.hg19.vcf > output.vcf