Cancer driver mutations Identification from VCFs

Question

[David_emir]

Hi All,

I have merged.VCF(Around 45) file of a particular type of brain tumor sequenced from around ~45 patients. I have received only VCF files from the vendor and I don't have any .bam or .fasta/q files available. So my question is, can I apply any method/s or can I use any tool/s on the .vcf file to remove variants which are not significant or to identify driver mutations in cancer development.

Secondly, can I clean(filter out unwanted mutations/germ cell mutations)out these .vcfs. So that I will end up in mutations which are significant( I don't have .BAM/FASTQ file to apply stringent variant call and then create a cleaned .vcf)

Can you guys please suggest me any pipeline or tools available to carry out this analysis?

Thanks a lot for your help!

Dave.

Answer 1

[Collin]

I would recommend checking out OpenCRAVAT. You can annotate your variants directly from VCF files to obtain the consequence type, driver mutation predictions (through CHASMplus), and annotate population allele frequencies in case some of your mutation calls may be germline variants. There's also many more annotations (see here).

[David_emir]

Hi Collin, thanks a lot for your help, I need your help in 20/20+ algo,here Thanks a lot, Have a great day! Dave.