Hi everyone,
I have both exome sequence data and human core exome chip data for the same samples and I wanted to measure discordance between them. Theoretically, discordance should be very low for the same samples, but I am getting very high values (~40% discordance). I should note that my sequence data contains no homozygous reference calls, but the chip data does. However, I only chose to run discordance on the sites that overlapped between sequence and chip data.
Any help is appreciated.
Thank you
I have both exome sequence data and human core exome chip data for the same samples and I wanted to measure discordance between them. Theoretically, discordance should be very low for the same samples, but I am getting very high values (~40% discordance). I should note that my sequence data contains no homozygous reference calls, but the chip data does. However, I only chose to run discordance on the sites that overlapped between sequence and chip data.
Any help is appreciated.
Thank you