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BJ-VariantAnnotation

Background#

The Variant Annotation Pipeline is unique and an essential tool to further understand your experimental analyses. Annotation is super import when it comes to identifying different cell types and genomic variant changes. This pipeline will take you a step further into your analyses by the incorporation of multiple Genomic and Cancer database such as The Single Nucleotide Polymorphism Database(dbSNP) and Catalogue of Somatic Mutations in Cancer(COSMIC) to help elucidate your scientific discoveries. The Variant Annotation Tertiary pipeline is dependent on the Secondary BJ-WGS-pipeline. Once the BJ-WGS-Pipeline completes successfully, the prerequisites are met to launch the Variant Annotation pipeline.

Key Components#

dbSNP: The Single Nucleotide Polymorphism Database is a public data base that contains SNPS across the the human genome. These can consist of single base nucleotide substitution and other multi bases deletions and insertions.1 More information on dsSNP can be found here

COSMIC: Catalogue of Somatic Mutations in Cancer is a cancer data base that includes somatic mutations across the human genome in cancer patients. This data base can identify somatic mutations base d off of gene name and cancer type, etc.2 More information on COSMIC can be found here

ClinVar: Is a documentation database that outputs reports to show the connection between human variation and phenotypes based on patient data and clinical evidence. Clivar takes allelic data that has been aligned to a reference set and produces and report based on the Human Genome Variation Society standards.3 More information on ClinVar can be found here

HGV: Human Genome Variation Society is a group the strives to discover and identify human genomic variation across populations and collaborates with ClinVar for reporting documentation. More information on this society can be found here

Parameters/Modules#

Parameter Name Options Description
Genome GRCh38 (default) Reference genome to use for alignment
Mode genic-variants (default) Reference genome to use for alignment
Variant Effect Prediction Tools Annotate the variants with SIFT, FATHMM, PROVEAN,LRT,and MutationTaster scores

Output files#

Output Directory/File
 Notes
tertiary_analyses/
      variant_annotation/
          *_snpEff.ann.vcf/
          *_snpEff.csv/
          *rnavariants_dnascope.vcf.gz /
          *rnavariants_haplotyper.vcf.gz		 This section includes the output files

Reference#

  1. Kitts, Adrienne, and Stephen Sherry. The Single Nucleotide Polymorphism Database (DbSNP) of Nucleotide Sequence Variation. National Center for Biotechnology Information (US), 2011. www.ncbi.nlm.nih.gov, https://www.ncbi.nlm.nih.gov/books/NBK21088/.

  2. Tate, John G., et al. “COSMIC: The Catalogue Of Somatic Mutations In Cancer.” Nucleic Acids Research, vol. 47, no. D1, Jan. 2019, pp. D941–47. DOI.org (Crossref), https://doi.org/10.1093/nar/gky1015.

  3. Landrum, Melissa, et al. ClinVar. National Center for Biotechnology Information (US), 2013. www.ncbi.nlm.nih.gov, https://www.ncbi.nlm.nih.gov/books/NBK174587/.