The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
Using BAMOUT files to check HaplotypeCaller
In your documentation for this you say "You can see that the bamout file, on top, contains data only for the ActiveRegion that was within the analysis interval specified by -L. The two blue reads represent the artificial haplotypes constructed by HaplotypeCaller (you may need to adjust your IGV settings to see the same thing on your machine). "
What are the IGV settings to see the artificial haplotypes?