YussAb / civic

CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.

CIVIC ANNOTATOR

• As a first step you need to download the vcf from civic repo

  • wget https://civicdb.org/downloads/01-May-2021/01-May-2021-civic_accepted_and_submitted.vcf

• Then we run

  • civicPreprocess.sh [01-May-2021-civic_accepted_and_submitted.vcf]

• Thew you need to activate conda and install vcfanno

  • civicAnnotator.sh [example/tumor_sample.BRCA.vcf.gz]

• You'll find the annotation at tumor_sample.BRCA.vcf.gz_civic.vcf