Illuminator
These programs help to convert Illumina files to Affymetrix like files that can then be used to with AutoSNPa or IBDfinder.
About program 1
This program is designed to convert Illumina SNP genotype files to Affymetrix like files. This means that the data can
then be used in any program designed to work with Affymetrix. I have no Illumina data and they have not responded
to emails asking about their data format therefore I can not guarantee this program will work with all Illumina files.
This program was created following a request from someone out side the department and said it worked correctly. If you
have any problems or have a different file format, email me and I can normally produce a program to help you with in a
few days.
This program works with files that have the format shown in the table below. The files initially came as '*.csv' but where
converted to '*.txt' file via excel.
| Column 1 | Column 2 | Column 3 | Column 4 | Column 5 | Column 6 | Column 7 |
| SNP name | Sample ID | Chromosome | Position | Allele 1 | Allele 2 | GC content |
| RS10938 | 400101 | 1 | 2016609 | A | B | 0.87897 |
| RS54678 | 400101 | 1 | 2503078 | B | B | 0.81167 |
Table 1
This program can be downloaded from here.
About program 2
This program is designed to convert an Illumina SNP genotype file with multiple individuals data to Affymetrix like files.
As with the first program this program may not work with your data, if not you can email me and I'll try to help.
This program was created following a request from someone out side the department and said it worked correctly. If you
have any problems or have a different file format, email me and I can normally produce a program to help you with in a
few days.
This program works with files that have the format shown in table 2 below.
| Column 1 | Column 2 | Column 3 | Column 4 | Column 5 | Column 6 | Column 7 | Column 8 | Column 9 |
| SNP name | Chromosome | Position | Inividual 1 | Allele frequency | LogR Ratio | Inividual 1 | Allele frequency | LogR Ratio |
| Name | Chr | Position | 0000000001.GType | 0000000001.B Allele Freq | 0000000001.Log R Ratio | 0000000002.GType | 0000000002.B Allele Freq | 0000000002.Log R Ratio |
| snp 1 | 1 | 1000000 | AA | 0 | 1.699783 | BB | 0 | 0.5525442 |
| SNP 2 | 1 | 2000000 | AB | 0 | 2.107005 | AA | 0 | 0.6255576 |
| SNP 3 | 1 | 3000000 | BB | 0.034345 | 0.9958471 | AA | 0 | 0.53003 |
| SNP 4 | 1 | 4000000 | BB | 0.5951048 | -1.469687 | AB | 0 | 0.4642296 |
Table 2
This program can be downloaded from here.
About program 3
This program converts Illumina data files when the positional data is stored in a different file to the genotype data and the genotype file contains
data for MULTIPLE individuals. The format of the SNP map file is shown in Table 3 and the format of the genotype file in Table 4.
| Column 1 | Column 2 | Column 3 | Column 4 | Column 5 |
| SNP name | Inividual 1 | Inividual 2 | Inividual 3 | Inividual 4 |
| [Header] | | | | |
| BSGT Version | 03/02/1932 | | | |
| Processing Date | 6/16/2009 11:46 AM | | | |
| Content | | HumanHap550v3_A.bpm | | |
| Num SNPs | 561466 | | | |
| Total SNPs | 561466 | | | |
| Num Samples | 4 | | | |
| Total Samples | 4 | | | |
| [Data] | | | | |
| HG_WUE_NRAA | HG_WUE_NRFN | HG_WUE_NROR | HG_WUE_NR-Fet |
| MitoA10045G | AA | AA | AA | AA |
| MitoA10551G | AA | AA | AA | AA |
| MitoA11252G | BB | BB | AA | BB |
| MitoA11468G | AA | AA | AA | AA |
| MitoA11813G | -- | AA | AA | -- |
Table 3: Genotype data file
| Column 1 | Column 2 | Column 3 | Column 4 | Column 5 | Column 6 | Column 7 | Column 8 | Column 9 |
| Index | Name | Chromosome | Position | GenTrain Score | SNP | ILMN Strand | Customer Strand | NormID |
| 1 | MitoA10045G | M | 10045 | 0.7355 | [T/C] | Bot | Top | 0 |
| 2 | MitoA10551G | M | 10551 | 0.7128 | [A/G] | Top | Top | 0 |
| 3 | MitoA11252G | M | 11252 | 0.7452 | [T/C] | Bot | Top | 0 |
| 4 | MitoA11468G | M | 11468 | 0.7345 | [T/C] | Bot | Top | 0 |
Table 4: SNP map file
This program can be downloaded from here.
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