Does IGV perform filtering when displaying reads?

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M Carta

• March 03, 2024 18:44

I have noticed that the read counts displayed in IGV are slightly lower than those in the AD field in the respective VCF files. Is it possible that IGV does not display certain reads (perhaps poor quality reads) and is there a way to adjust any cut-offs?

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  Gökalp Çelik

  • March 03, 2024 19:36

  Hi M Carta

  Yes it does. If you are using the desktop IGV, options can be set at the preferences pages under View -> Preferences -> Alignment tab. 

  By the way those AD numbers may still not match what you observe under IGV. You may check the article below for more details.

  https://gatk.broadinstitute.org/hc/en-us/articles/360035532252-Allele-Depth-AD-is-lower-than-expected 

  Regards. 

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