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Illumina / ExpansionHunter

A tool for estimating repeat sizes
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Realigned BAM visualization #111

Closed apredeus closed 3 years ago

apredeus commented 3 years ago

Hello,

I was trying to visualize the realigned reads, but it seems like the format is off somehow - IGV is not able to visualize the reads. I can't seem to spot why. Any suggestions?

Thank you in advance!

egor-dolzhenko commented 3 years ago

Hi Alex,

Yes, unfortunately IGV won't be able to visualize graph-realigned reads. We have a special tool for this: https://github.com/Illumina/GraphAlignmentViewer/

Note that we are planning to release a new visualizer for ExpansionHunter in a few weeks.

I hope this helps. If you have any feedback on the visualization tool or ExpansionHunter itself please us know. Egor

apredeus commented 3 years ago

Thank you! I've obtained a strange result and I'm not sure how to interpret it. I get heterozygous 43 unit repeat identified at PHOX2B (it's a MGI 60x PCR-free genome). Visualization looks like this. Does this look like an artifact? Thank you in advance!

image

egor-dolzhenko commented 3 years ago

Thanks for sharing the plot! Yes, this looks like a data artifact since reads supporting the 43 unit repeat are of low quality. (Note that our software is designed for and tested on Illumina PCR-free WGS.)