igv and vcf difference

Question

[biology_inform]

Hi, I am trying to find point mutations from my bam files but the output is given by vcf and IGV is different. Some mutations in igv file are not in vcf file. So I wonder; when the vcf file is being created is there a filtering based on quality for example?

Answer 1

[ATpoint]

So I wonder; when the vcf file is being created is there a filtering based on quality for example?

Yes, usually variant callers apply a lot of filters. Check the documentation of the caller you used.