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Illumina / ExpansionHunter

A tool for estimating repeat sizes
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Using different input bam files #139

Closed MeiShu00 closed 3 years ago

MeiShu00 commented 3 years ago

Hi,

I understand that BAM or a CRAM file with alignments of reads from a PCR-free WGS sample is one of the required inputs.

Hence, would like to ask the following questions:

  1. Will ExpansionHunter work with PCR-amplified targeted STR?
  2. Why are reads from a PCR-free WGS sample required?

Thanks !

egor-dolzhenko commented 3 years ago

Thanks for the questions!

ExpansionHunter (EH) assumes that sequencing coverage is relatively uniform throughout the repeat region (hence the requirement for PCR-free WGS).

EH will run on PCR-amplified data, however, some repeats may not be genotyped correctly. For example, long 100% GC repeats are very difficult to amplify with PCR.

Visualization tools like REViewer can help to visually investigate sequencing data in repeat regions of interest: https://github.com/Illumina/REViewer

Did I answer your questions? Please let me know if there is anything else you'd like to know.

Best wishes, Egor

MeiShu00 commented 3 years ago

Dear Egor,

Yes, my questions are answered ! Thank you !