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Last pushed: 2 years ago
Short Description
Annotate called variants (VCF format) with snpEff
Full Description

download the example input data

wget -O - ftp://gsapubftp-anonymous@ftp.broadinstitute.org/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

Docker Pull Command
Owner
j5kim

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