generate ANNOVAR input file from EXCEL

Question

[giovannadv]

Hello,

I need some help. I have to annotate a list of variants in a excel table; how can I transform in a input file for ANNOVAR? I've transformed it into txt document with tab separators but then can I use -convert2annovar.pl?

THANK YOU in advance for your kind help!

Gio

[bibb77]

Can you please provide an example for your list of variants?

[giovannadv]

I've create an excel file where the first 5 columns are the chromosome, the start position, the end position, the ref allele and the alt. allele... the other columns are empty... ex: 6 1052293 1052293 A G 7 59666859 59666859 T C ecc Can You help me?... Tanks! Gio

Answer 1

[NB]

convert2annovar.pl is used only when you you have your files in one of the following formats.

So in order to run the annovar program, your input file needs to have the following mandatory columns. If your excel sheet has the below info, then you can just re arrange the columns and transform it to a text file to run annovar.

chr    position    position    allele1    allele1
1      948921      948921      T          C
1      1404001     1404001     G          T

Hope this helps!

[giovannadv]

I will try... hope it will work! THANK YOU!!