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-   -   Annovar variant filtering (http://seqanswers.com/forums/showthread.php?t=71232)

tristan dubos 09-02-2016 01:58 AM

Annovar variant filtering
 
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_ 09-02-2016 04:31 AM

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 09-02-2016 04:47 AM

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


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