Users' documentation for IGC in Python

Installation

This software requires Python3 to be installed. After you have succesfully obtained the archive you can execute the following command from a terminal to unzip the program:

• gunzip igc.py.gz

Execution

To use IGC, write the following command line:

python3 igc.py <filename>

where <filename> is the input file with raw intensities of an individual in extended make ped format (only one line)

Intensities extended mkeped format of the input file

A text file of SNP data set, in post-makeped format as described here:

One row per individual (ony one individual is allowed by IGC), 7 + 2xTotalSNPs columns, with TotalSNPs being the number of SNPs. Columns must be separared by a blank or tab character.Each column must contain an integer corresponding to the value of raw intensity for A or B allele. See an example of a file in .iou format. IGC will only allow one individual, i.e. the input.iou file must have only one row.

Description of columns:

• Column 1: family code
• Column 2: individual code
• Column 3: father code (0 if the individual is not a child)
• Column 4: mother code (0 if the individual is not a child)
• Column 5: gender
• Column 6: affection status
• Column 7: another individual id
• Columns 8 until 7+2*TotalSNPs: SNP intensity values (each SNP uses two contiguous columns). Example: if SNP1 A and B intensity values for an individual are respectively 333444 and 832, column8 will have the value 333444 and column9 will have the 832.

Output for the program IGC

The output will be written in a file placed in the same folder where the input file is placed, and with extension _igc.gou.
The file is in extended makeped format (gou file), although this time genotype values allowed are only 0 0 for missing, 1 1 for AA, 1 2 for AB and 2 2 for BB genotypes:

Extended mkeped format of the output file

A text file of SNP data set, in post-makeped format as described here:

One row per individual (ony one individual is allowed by IGC), 7 + 2xTotalSNPs columns, with TotalSNPs being the number of SNPs. Columns must be separared by a blank or tab character.Each column must contain an integer. See an example of a gou file.

Description of columns:

• Column 1: family code
• Column 2: individual code
• Column 3: father code (0 if the individual is not a child)
• Column 4: mother code (0 if the individual is not a child)
• Column 5: gender
• Column 6: affection status
• Column 7: another individual id
• Columns 8 until 7+2*TotalSNPs: SNPs values (each SNP uses two contiguous columns). Example: if SNP1 value for an individual is 12 (heterozygous), column8 will have the value 1 and column9 will have the 2.