Association peak plotting

Basic help

singularity exec <singularity options> <annotator container name> plotpeaks -h

Usage: plotpeaks -t <p-value threshold>
                 -i <input association file>
                 -c <chromosome column name>
                 -p <p-value column name>
                 -m <MAF column name>
                 --id <variant ID column name>
                 --a1 <allele 1 column name>
                 --a2 <allele 2 column name>
                 --pos <variant position column name>
                 --plink <comma separated PLINK prefixes>
                 --flank <flank size (bp)>: optional, default: 500000
                 --dbsnp <dbSNP VCF>: optional
                 -h : print this help and exit

VarAnnot - a simple variant annotation tool

A variant annotation pipeline that combines information from various sources to get a better understanding of the discovered associations.

Currently following sources are queried:

• ENSEMBL
• PubMed
• UniProt
• GTEx
• GWAS Catalog
• GnomAD
• MGI mouse database
• Gene Expression Atlas

Following functional scores are used for annotation:

• GWAVA
• SIFT
• PolyPhen

Basic help

singularity exec variantAnnotator <command> -h

where command is one of:

1. prepareData
2. annotate

Workflow

1. Download GWAVA script from Sanger. On AK GWAVA is installed in /storage/hmgu/software/gwava/

2. Download and process data from ENSEMBL Regulation, GWAS Catalog and GTEx using prepareData command. On AK prepared data are in /storage/hmgu/referenceData/variant_annotator_data/

3. Perform variant annotation using annotate command.

Example: singularity exec -B /tmp -B ~ -B /storage/hmgu/ /storage/hmgu/containers/worker_2.5 annotate -v debug -i rs12570947 -o ~/output -d /storage/hmgu/referenceData/variant_annotator_data/ --html -g /storage/hmgu/software/gwava/

The above command will create rs12570947.html and rs12570947.log in ~/output directory