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Illumina / ExpansionHunter

A tool for estimating repeat sizes
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ExpansionHunter for PCR-not-free protocol #104

Open golubnikova opened 4 years ago

golubnikova commented 4 years ago

Hi! Thank you for your great tool! I have the same question as here. Could I use ExpansionHunter for samples prepared with PCR-not-free protocol? I'm using Nextera DNA Flex protocol for WGS. I've tried to run ExpansionHunter - it works, test.log and test.json.txt files are attached. How could I understand that ExpansionHunter works correctly?

Expansion Hunter v2.5.5

Originally posted by @golubnikova in https://github.com/Illumina/ExpansionHunter/issues/35#issuecomment-674709368

egor-dolzhenko commented 4 years ago

Thank you for the question! Although we don't officially support PCR+ data, we know of groups that have shown that ExpansionHunter can detect expansions of many repeats in PCR+ data well. As a general rule of thumb, 100% GC expansions will be hard to detect since they might not get amplified in PCR+ data.

A good (but very manual) way to evaluate a given genotype call is to visualize alignments of reads with GraphAlignmentViewer:

https://github.com/Illumina/GraphAlignmentViewer/

If it is permissible for you to share the images generated by GraphAlignmentViewer, we would be happy to assist with interpreting them. In which case please feel free to send them by email (edolzhenko@illumina.com).

Best wishes, Egor