IGV coverage bar has color, but no mutation?

Question

[chrisgr]

I attached a screenshot of an IGV output, what could be the reason(s) for the coverage bar to havea color but no mutation was detected? (4 total all G)

[Nicolas Rosewick]

I guess G is not the reference allele on the genome

[chrisgr]

Thanks for your response! Sorry I messed up, you're right. I wanted to post a very simple example of what I was struggling with. Let me try again with a new one. Why does the G mutation have a color in the coverage bar and the T at the left does not? or what could be potential reasons for it?

Answer 1

[Nicolas Rosewick]

From IGV doc :

If a nucleotide differs from the reference sequence in greater than 20% of quality weighted reads, IGV colors the bar in proportion to the read count of each base (A, C, G, T).

https://software.broadinstitute.org/software/igv/AlignmentData

[chrisgr]

Yes that's it thanks so much!

Answer 2

[Amitm]

This is possibly due to the threshold in the IGV preferences pop-up menu --> Alignments tab --> scroll down to 'Coverage Track Options' --> in there 'Coverage allele fraction threshold'. I think, by default its set at 0.2. So if variant allele fraction is <20%, the coverage track wouldn't show colour difference. If you expect (or think relevant), put it to something lower, like 0.05

[chrisgr]

Yes 20% seems so high, I received VCF files from Novogene, and the VCFs also have this 20% threshold (only contain mutations with 20%+ alt). I can't do a somatic analysis myself based on those VCf files because I can't see if the mutation is there in the control VCF (even though it's 1 or 2%). I don't see why they would do that.