Annovar to maf

[shhabnsbwjd]

Hello,

I am trying to import my variant file with all the required maf columns in R studio 'Chr Start End Ref Alt Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAChange.refGene Tumor_Sample_Barcode Func.refGene' using this code;
var.annovar2 <- system.file("extdata", "mutation.hg19_multianno.txt", package = "maftools")

But imported file is empty

Kindly can someone help me please what am missing. I really need help

Thank you

[PoisonAlien]

Hi,

You dont have to use system.file(). It is only required to access the example file bundled with the maftools package.
You can directly use the annovarToMaf() to process your mutation.hg19_multianno.txt file.

annovarToMaf(annovar = "mutation.hg19_multianno.txt")

[shhabnsbwjd]

It worked.... Thank you so much. And what if I want to use my vcf file??

[PoisonAlien]

VCF files are not supported for now. You will have to convert them into MAF. Checkout vcf2maf.

[shhabnsbwjd]

Thank you so much

On Tue, 5 Jul 2022 at 04:42, Anand Mayakonda ***@***.***> wrote: Hi, You dont have to use system.file(). It is only required to access the example file bundled with the maftools package. You can directly use the annovarToMaf() to process your mutation.hg19_multianno.txt file. annovarToMaf(annovar = "mutation.hg19_multianno.txt") — Reply to this email directly, view it on GitHub <#844 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AZ5F24F3YTRFVWFH64FNM63VSOVKHANCNFSM52TO4HBQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- *Maryam Shah* PhD Student, Peninsula Medical School, Faculty of Health, University of Plymouth, UK