gnomad_annotation

Python package to add gnomAD allele frequencies to MGI annotated files

• gnomAD exome and genome information are provided separately
• Preserves all non-redundant columns from the input file

Things to note about gnomAD

• Does not provide Y chromosome information
• Allele counts, numbers and frequencies provided by this script are filtered high quality genotypes, not raw counts (GQ >= 20, DP >= 10, allele balance > 0.2 for heterozygote genotypes), previously referred to as adjusted allele frequencies for ExAC
• Read more

Uses Ensembl VCF files as initial source.

• Source: ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/ GRCh[version]/variation_genotype/gnomad.[version].vcf.gz
• Provides smaller files than gnomAD directly
• Provides GRCH38 liftover coordinates
• Imported to an MGI allocation using https://github.com/genome/genome/blob/master/lib/perl/Genome/Db/Ensembl/Gnomad.pm

VCF files are first processed and stored in trie structures for fast annotation

• vcf_to_pickle.py
• Initial creation takes ~1 day for genomes file

Code is currently actively developed, use at your own risk

• There is no lower limit on the number of alleles contributing to the allele frequency provided
• Alleles not found and alleles with no information (no high quality genotype data) are annotated with NA