How to achieve Variant filtering?

Question

[Sharanya]

Using CLC Genomics Workbench, I have successfully run some fastq sequences and got the 'Final Annotated variants' in an excel sheet. However, I want to filter these to keep and detect only those with actual clinical relevance to Neuroblastoma. Is there a way to do it?

I need to filter out the artifacts using either gnomAD, COSMIC, or REVEL databases, but I do not know how to do it.

Also, is there a way to generate a black list and use the population frequency to filter out the variants?

Answer 1

[Istvan Albert]

bcftools offers many utilities to filter variants,

https://samtools.github.io/bcftools/bcftools.html

another alternative is vcflib

https://github.com/vcflib/vcflib