I am now cleaning the illumina custom MS exome array chip (about 330k SNPs). Basically, i import the raw data into Genomestudio, recluster and import data into Plink format. All the sample genotype call rate (>98%). However, I found in the bim file, 527 SNPs with the first column(chromosome information) marked as 0. I am confused what does this mean? why would this happen? see below example
0 MS_Replication_Chip_chr1-reichrank1555 0 993 0 G
Also i found we have about 150k SNPs are monomorhic, is this correct?
Any one have any suggestions?