VEP and future analysis

Question

[Roy]

Hello all,

I am working on a script using VEP to filter down by 1.5 million variants reads to an actual plausible number, as well as planning what future analysis I can do. Using filters such as setting biotype to protein_coding, pathogenic predictors, and gnomAD_AF, I can narrow my variants down to about 1000. Are there any other recommended filters that the community can share to get this 1000 variants number even lower? This is searching for cancer variants, so maybe a subset of genes? Any feedback is helpful.

Thanks

[abedkurdi10]

what value of gnomAD_AF are you using to filter out variants? you can lower it down to 0.01 (0.1%). Just give it a try.