Cohort

The path to the cohort data is specified using the -c or --cohort flag and specifying this input requires -i or --index to be supplied. Every individual in the cohort will be compared to each allele passed under the --indexflag.

    -c, --cohort <cohort>
        Cohort of individuals for which all measures will be calculated
    -i, --index <index>...
	Index allele used for cohort calculations only, all individuals will be compared to these alleles

The required column is id or ID. The HLA allele columns can be any of A1, A2, B1, B2, C1, C2 where 1 and 2 represent the two alleles an individual has for that specific gene/locus. In addition to the HLA allele the KIR columns should be specified of the format KIR2DL1 or 2DL1, KIR2DL2 or 2DL1 etc., see the Nomenclature section for the KIR columns names that are allowed and the HLA allele names that can be specified in the A1 to C2 columns.

Alternative names are allowed for some of the columns and are listed below:

• ID = id, sample, rowid
• A1 = A.1
• A2 = A.2
• B1 = B.1
• B2 = B.2
• C1 = C.1
• C2 = C.2
• KIR2DL1 = 2DL1
• ..
• KIR3DL2 = 3DL2

The KIR columns can have the following values represent the presence or absence of a gene:

• Presence = 1, TRUE, Y, T
• Absence = 0, FALSE, N, F

An example cohort file with the column names can be seen HERE.