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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 1Column 2Column 3Column 4Column 5Column 6Column 7
SNP nameSample IDChromosomePositionAllele 1Allele 2GC content
RS1093840010112016609AB0.87897
RS5467840010112503078BB0.81167

Table 1

insilicase icon 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 1Column 2Column 3Column 4Column 5Column 6Column 7Column 8Column 9
SNP nameChromosomePositionInividual 1 Allele frequencyLogR RatioInividual 1 Allele frequencyLogR Ratio
NameChrPosition0000000001.GType0000000001.B Allele Freq0000000001.Log R Ratio0000000002.GType0000000002.B Allele Freq0000000002.Log R Ratio
snp 111000000AA01.699783BB00.5525442
SNP 212000000AB02.107005AA00.6255576
SNP 313000000BB0.0343450.9958471AA00.53003
SNP 414000000BB0.5951048-1.469687AB00.4642296

Table 2

insilicase icon 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 1Column 2Column 3Column 4Column 5
SNP nameInividual 1 Inividual 2 Inividual 3 Inividual 4
[Header]
BSGT Version03/02/1932
Processing Date6/16/2009 11:46 AM
ContentHumanHap550v3_A.bpm
Num SNPs561466
Total SNPs561466
Num Samples4
Total Samples4
[Data]
HG_WUE_NRAAHG_WUE_NRFNHG_WUE_NRORHG_WUE_NR-Fet
MitoA10045GAAAAAAAA
MitoA10551GAAAAAAAA
MitoA11252GBBBBAABB
MitoA11468GAAAAAAAA
MitoA11813G--AAAA--

Table 3: Genotype data file

Column 1Column 2Column 3Column 4Column 5Column 6Column 7Column 8Column 9
IndexNameChromosomePositionGenTrain ScoreSNPILMN StrandCustomer StrandNormID
1MitoA10045GM100450.7355[T/C]BotTop0
2MitoA10551GM105510.7128[A/G]TopTop0
3MitoA11252GM112520.7452[T/C]BotTop0
4MitoA11468GM114680.7345[T/C]BotTop0

Table 4: SNP map file

insilicase icon This program can be downloaded from here.



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