This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Annovar file to maf file conversion

Hi everyone,

Can anyone help me with troubleshooting annovar to Maf file generation?

I am using this command in R but I am getting error.

annovarToMaf(annovar, Center = NULL, refBuild = "hg19", tsbCol = NULL,
  table = "refGene", basename = NULL, header = FALSE, sep = "\t",
  MAFobj = FALSE)
maf r annovar
• 1,434 views • link
updated by Ram Ram • written by ganeshram • ganeshram

And the error is...

• 0 views • link
written by Asaf Asaf

the error I am facing is this.

annovarToMaf("Desktop/Galaxy/PY-3_indel_myanno_hg38_multianno.txt", Center = NULL, refBuild = "hg19", tsbCol = NULL, table = "refGene", basename = NULL, header = FALSE, sep = "\t", MAFobj = FALSE) Error in annovarToMaf("Desktop/Galaxy/PY-3_indel_myanno_hg38_multianno.txt", : unused argument (header = FALSE)

• 0 views • link
written by ganeshram • ganeshram

Weird. Can you try and run maftools::annovarToMaf() to make sure you're using the right function and nothing ran over its declaration? Also check that you have the latest version.

• 0 views • link
written by Asaf Asaf

0 answers

No answers yet.

Log in to answer this question.

More posts like this