I'm interested in converting my PED/MAP files to BED/BIM/BAM files to perform association testing. However, my PED file contains missing values coded as "-9" in addition to the affection statuses 1 (absent) and 2 (present), as illustrated below:
IND1 IND1 0 0 1 1 2 1 2 2 -9 -9 -9 -9 -9 -9 -9
IND2 IND2 0 0 1 1 -9 -9 -9 -9 -9 -9 -9 -9 2 2 1
IND3 IND3 0 0 1 2 -9 -9 -9 -9 -9 -9 -9 -9 2 2 1
etc.
I used the command line "plink --file FILENAME --make-bed --out FILENAME" and the conversion worked, but as output I get a BIM file containing "-9" in some of the last 2 columns (allele1 and allele2), even if the PED file contains non-missing values for these marker IDs.
19 ID1 0 55187279 -9 2
19 ID2 0 55188593 2 -9
19 ID3 0 55188593 -9 1
I don't understand why, and how can I get rid of this issue. I hope someone can help me to find a solution. Thank you in advance!
Try with the "--missing-genotype -9" option.