I am try to use the aye-aye SNP dataset available in galaxy. However, the genotype for some of the SNPs is -1 (rather than 0, 1, or 2). Do you know why this is and should those data be omitted?
This value represents a missing or unavailable data in the gd_snp file format. Please see: http://www.bx.psu.edu/miller_lab/docs/formats/gd_snp_format.html
Best, Jen, Galaxy team