top hits annotation

Annotation of tophits

For top hits SNPs / loci the pipeline performs automatic annotation with overlapping genes and nearby genes.

The maximum distance between the variant / locus and the sorrounding annotated gene is set with the parameter annotation_interval_kb (25kb by default). Genes located +/- defined kb from the SNP / locus are annotated as nearby genes.

Pre-made BED files for gene annotation are available for GRCh37 and GRCh38. These files are generated from the GENCODE annotation version 39. When performing annotation one can chose to annotate for all genes or only protein coding genes by setting the genes_group parameter to all or protein_coding respectively. By default, the pipeline will annotate for protein coding genes.

If you want to use a different annotation file, you can provide custom gene definition with the genes_bed and genes_ranges parameters. In this case the pre-made annotation files will not be used. For this you need to provide:

• genes_bed: a regular tab-separated BED file (chromosome, start, end; zero-based), with gene names in the 4th column. Note that a name must be present for all genes.
• genes_ranges: essentially the same as above but space separated.