This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Show mismatches for specific positions in AlignmentsTrack of Gviz package

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

0 answers

No answers yet.

Log in to answer this question.