Huge Number Of Mendel Errors In Plink

Question

[srijani.sridhar]

Hello,

I have raw gene reports from Illumina 1M platform ("final report.txt") that I converted to .map and .lgen formats for PLINK. Upon filtering for Mendel errors (--me 1 0.05), almost 87% of my markers are being removed. Is it because my gene reports contain cnv information too? Or is it because of something else I'm missing?

[Pierre Lindenbaum]

http://en.wikipedia.org/wiki/Parental_testing :-)

[Matt Shirley]

This does tend to come out during consent, but sometimes the parent must think the researchers will just throw away the data when they realize "dad" is not dad.

Answer 1

[srijani.sridhar]

alright, thank you! also, does the MAP file have to contain only snps? is it okay for it to have cnvs too?