Analyzing VCFs

Question

[Roy]

Hello all,

I am in a dilemma where I can get FASTQ's from TSO500 that can be uploaded to a software and outputs potentially pathogenic variants as well as VUS. However, sometimes I obtain just a VCF and am trying to filter out the thousands of variants to see if I can obtain any useful info. I am playing around in VEP to see if I can filter this effectively, such as using concerning SIFT/Polyphen/CADD scores, canonical variants, and other characteristics. Is there a better way to do this?

Thanks, Roy

Answer 1

[milad eidi]

hello Roy

In the context of human variants, there is lots of options. As a web based tool, i recommend, FRANKLIN database, it takes your vcf file and your patient phenotypes, after a while, the most important variants will be reported.

As a standalone tool, ANNOVAR is absolutely perfect. you can make what local databases you want for annotation purpose or download and use its latest free downloadable databases.

hope it helps, Milad Eidi

[Roy]

Hello Milad,

FRANKLIN database is phenomenal for my task. Thank you so much!