Show mismatches for specific positions in AlignmentsTrack of Gviz package
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15 months ago
Irsan ★ 7.8k

Using the Gviz package, I can create visualization of reads mapped to a reference sequence and show mismatches bases, so that you can see if there are mutations in my sample. As I am often working with oxford nanopore sequencing data, my base call accuracy isnt great and in my alignment track I see a lot of noise (random mismatches/INDELs). Therefore I want to configure for which positions I want to show mismatches. For example see the below image taken from Gviz user's guide, in the middle there clearly is a heterozygous mutation, and in the surrounding regions left and right some mismatches. SUppose I only want to show mismatches of the heterozygous mutation, how can I do that?

Show mismatches example from Gviz user guide

R bioconductor • 424 views
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