igv browser
What is the criteria used in igv to show the given variant is observed or not?
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sahalpaladan •
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what do you mean ? IGV is not a variant caller , it 'just' displays the bases
I understand IGV is used to visualize aligned reads. Let me rephrase my query above. I have observed few set of variants in my vcf file, and when I visualize those variants in IGV browser, nucleotide changes with >20% are displayed as false positive, however, if the observed nucleotide change is <=20%, IGV browser sometimes categorizing it as not false positive or sometimes as false positive. I'm not sure on what criteria it's segregating these values. Could you please clarify this?
Look, we cannot see your screen, not your file. Please show data and screenshots. What in your option is a false positive?