IGV is not showing the low frequency variants

Question

[k.manojkumar2991]

Hi,

I have called out low frequency variants using GATK, Samtools, VarSome and Mutect2. while visualizing it in IGV i cant see those variants. the variants was identified in all four variant calling tools. [STK11p.K262Rfs*22] Read coverage = 458 mutated coverage = 20. can any one help me to sort out the this issue. How to visualize the low frequency variants in IGV. Thank you in advance.

[Pierre Lindenbaum]

https://software.broadinstitute.org/software/igv/Preferences Downsampling

IGV displays a specified number of randomly sampled alignments configured by the downsampling parameters instead of keeping all of them in memory. The coverage track, displaying total coverage at a region, is unaffected; that is, it always shows unsampled values. Default setting downsamples up to 100 per 50 nt window and paired reads are downsampled as a set.

also, in preferences/alignments show all your reads (duplicates, secondary etc...)

[k.manojkumar2991]

Thank you, I tried with down sampling still now I can't able to visualize the exact variants called by the variant calling tools