vcf2maf VEP annotated VCF conversion
2
1
Entering edit mode
4.2 years ago
Martina ▴ 30

Dear all, I heard many times about possibility to convert annotated vcf to maf with vcf2maf by rewriting of name to *.vep.vcf (which marks that vcf is already annotated). But even when I do it, the vcf2maf program wants to annotate it again, which I don't want. Can you please advice me how to make it work without annotation?

$ vcf2maf.pl --input-vcf input.vep.vcf --output-maf output.vep.maf --vcf-tumor-id input_TUMOR --vcf-normal-id input_NORMAL --tumor-id input_TUMOR normal-id input_NORMAL --buffer-size 100  --ref-fasta

/exports/eddie/scratch/s1959373/external/human_g1k_v37.fasta --filter-vcf 0

STATUS: Running VEP and writing to: ./input.vep.vep.vcf
ERROR: Cannot find VEP script in path: /home/..

Thank you very much!

Martina

vcf2maf ngs vcf maf wgs • 3.5k views
ADD COMMENT
0
Entering edit mode

@martina I was wondering if you have solved the problem. I have vep.vcf file and want to convert it into MAF.

ADD REPLY
0
Entering edit mode

Hello, yes, the answer is just in the comment below: Hello, this issue said you need to COPY your vcf and name "*.vep.vcf", not mv command.

So you need to have both .vcf and .vep.vcf files in the folder.

Have a nice day, Martina

ADD REPLY
0
Entering edit mode
4.2 years ago
MatthewP ★ 1.4k

Hello, this issue said you need to COPY your vcf and name "*.vep.vcf", not mv command.

ADD COMMENT
0
Entering edit mode
4.2 years ago
Martina ▴ 30

Oh.. Thank you very much :)

ADD COMMENT

Login before adding your answer.

Traffic: 2887 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