Annovar variant filtering

[tristan dubos]

He guys,
I m using convert2annovar.pl to convert vcf to avinput , and in this output i have only 14 variants against more then 1000 variants in the input.
Do you know witch filters apply convert2annovar.pl to reduce the number of variant ?

Best regards

Tristan

[vivek_]

I don't think there is a filter involved in the conversion, anyways you should get a .log file that tells you all that annovar did on the dataset.

[tristan dubos]

Thank you for the answer. There is not log file during the conversion (with default mode) i think the log file is create during the annotate_variation.pl