convert2annovar Skipped invalid alternative alleles found in input file

Question

[giovannadv]

Hi,

I' m a new user; I've tried to convert my vcf4 file withconvert2annovar file to obtain a input file to analize with ANNOVAR.

I' ve obtained my avinput file witha a Warning: Skipped 2 invalid alternative alleles found in input file

How can I know wich are the 2 alleles skipped?

Thank you for your kind help

Gio

Answer 1

[Jorge Amigo]

you can use the -v option from convert2annovar.pl to get all the description of the conversion. the information you're looking for will be listed as a WARNING, so you may want to grep WARNING the STDERR where all this information is dumped:

convert2annovar.pl -format vcf4 -v file.vcf 2>&1 | grep WARNING