Cancer driver mutations Identification from VCFs
1
0
Entering edit mode
2.6 years ago
David_emir ▴ 430

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.

cancer driver mutation vcf mcf • 771 views
ADD COMMENT
2
Entering edit mode
2.6 years ago
Collin ▴ 1000

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).

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 850 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6