PRELIMINARY DATA - USE WITH CAUTION
These files contain exome sequencing data on loss of function variants from 3782 East London Genes & Health volunteers (Bangladeshi and Pakistani, with self-stated related parents), 2624 Bradford volunteers (Pakistani, mostly self-stated or DNA autozygous individuals), 1060 Birmingham volunteers (Pakistani, unselected). Bradford and Birmingham samples are as described in Narasimhan et al Science 2016, with additional Bradford samples.
Exome sequencing was performed at the Wellcome Trust Sanger Institute. Standard WTSI alignment and GATK genotype calling pipeline. Note that in Narasimhan et al Science 2016 genotypes concordant in both GATK and samtools were described.
Both files have detailed variant annotation (from Ensembl Variant Effect Predictor) as well as allele frequencies in other populations, and from ExAC/gnomAD.
File 1 is homozygous predicted loss of function variants, only rare variants (MAF<1% in all samples), and only high call rate (>95%) variants. This is probably what you want to use for high quality knockouts. This is an excel file for ease of use (please let us know if excel has mangled any gene names or other data).
File 2 is all predicted loss of function variants, homozygotes and heterozygotes, rare and common, all call rates. This is a plain text zip file.
