Genotyping chips strand and build files

This page contains strand files for the common genotyping chips on a variety of genome builds, if you have a chip and/or build that is not listed here please contact me, Will Rayner (wrayner at well dot ox dot ac dot uk) and I can create and upload the required file.


Illumina data files
For the Illumina chips the zip file contains three files, the .strand file, the .miss file and the .multiple file. The strand file contains six columns, SNP id, chromosome, position, %match to genome, strand and alleles. The SNP ids used are those from the annotation file and so are not necessarily the latest from dbSNP. The alleles listed are the Illumina TOP alleles, if you are in any doubt whether your data file can be used with these strand files a check of the non A/T G/C SNPs alleles vs the strand file should confirm this for you. If there are differences then it is likely your genotype file has been created using a different set of alleles, in this case if you can provide a list of the SNP ids and their alleles on the chip it is likely a strand file can be created for you.
The .miss file gives the ids of the SNPs that did not reach the required threshold for mapping to the genome, the position and strand of the best match are given. The .multiple file contains SNPs that had more than 1 high quality match (>90%) to the genome, in this instance the better match is taken for the .strand file.
The strand files assume that your genotype calling algorithm has standardised the genotype allele calls to the Illumina TOP strand.

Other Allele Sets
Illumina chips are not always called using the TOP strand and if this is the case for your data file then the most likely alternative is using the alleles derived from the Source Sequence in the annotation file, I have labelled the files, where they exist, as SourceStrand and will be adding them as time, and demand, allows.

A script developed by Neil Robertson for updating the chomosome, position and strand of binary ped files using these strand and position files can be downloaded here:
update_build.sh

Usage is update_build.sh <bed-file-stem> <strand-file> <output-file-stem>
where:
 <bed-file-stem> is the name of your binary ped set minus the .bed, .bim or .fam extension
<strand-file> is appropriate strand file for you chip and current strand orientation (TOP, SOURCE, etc)
<output-file-stem> is the name of the new output file to create again minus the .bed, .bim or .fam extension

The ASHG 2011 Poster describing this can be downloaded here:
WR-ASHG2011posterPP-portrait.pdf

Allele Updates
If your genotypes are represented as A/B then the files present on this link allow you to update the alleles from A/B to TOP strand A, C, G, T calls, if the chip you are using is not listed contact me and I can create these files.
All files for the chips I have done so far are here this list will be updated in tandem with the strand and position files.

Ref/Alt
Experimental files listing the Ref allele for each Illumina chip can be found here
These are in plink format for use with the --reference-allele option

Strand and Position Files

HumanHap240S_11216501_A
BDCHP-1X10-HUMANHAP240S_11216501_A-b36-strand.zip
BDCHP-1X10-HUMANHAP240S_11216501_A-b37-strand.zip

HumanHap300v1-1_11219278_C
BDCHP-1x10-HUMANHAP300v1-1_11219278_C-b35-strand.zip
BDCHP-1x10-HUMANHAP300v1-1_11219278_C-b36-strand.zip
BDCHP-1x10-HUMANHAP300v1-1_11219278_C-b37-strand.zip
HumanHap300v1-1_11219278_C Source Strand Versions
BDCHP-1x10-HUMANHAP300v1-1_11219278_C-b35-Source-Strand.zip
BDCHP-1x10-HUMANHAP300v1-1_11219278_C-b36-Source-Strand.zip
BDCHP-1x10-HUMANHAP300v1-1_11219278_C-b37-Source-Strand.zip

HumanHap300v2_A
HumanHap300v2_A-b36-strand.zip
HumanHap300v2_A-b37-strand.zip

Human CNV370v1_C
HumanCNV370v1_C-b35-strand.zip
HumanCNV370v1_C-b36-strand.zip
HumanCNV370v1_C-b37-strand.zip
Human CNV370v1_C Source Strand Versions
HumanCNV370v1_C-b36-SourceStrand.zip
HumanCNV370v1_C-b37-SourceStrand.zip

HumanCNV370-Quadv3_C
HumanCNV370-Quadv3_C-b35-strand.zip
HumanCNV370-Quadv3_C-b36-strand.zip
HumanCNV370-Quadv3_C-b37-strand.zip
HumanCNV370-Quadv3_C-b38-strand.zip

HumanHap550_11218540_C
BDCHP-1X10-HUMANHAP550_11218540_C-b36-strand.zip
BDCHP-1X10-HUMANHAP550_11218540_C-b37-strand.zip

HumanHap550-2v3_B
HumanHap550-2v3_B-b35-strand.zip
HumanHap550-2v3_B-b36-strand.zip
HumanHap550-2v3_B-b37-strand.zip
HumanHap550-2v3_B Source Strand Versions
HumanHap550-2v3_B-b36-SourceStrand.zip
HumanHap550-2v3_B-b37-SourceStrand.zip
HumanHap550-2v3_B Ilmn Strand Versions
HumanHap550-2v3_B-b35-Illmn.strand.zip
HumanHap550-2v3_B-b36-Illmn.strand.zip
HumanHap550-2v3_B-b37-Illmn.strand.zip

HumanHap550v3_A
HumanHap550v3_A-b35-strand.zip
HumanHap550v3_A-b36-strand.zip
HumanHap550v3_A-b37-strand.zip
HumanHap550v3_A-b38-strand.zip

Human610Quadv1_B
Human610Quadv1_B-b35-strand.zip
Human610Quadv1_B-b36-strand-v1.zip
Human610Quadv1_B-b37-strand-v2.zip
Human610Quadv1_B-b38-strand.zip
Human610Quadv1_B Source Strand Versions
Human610-Quadv1_B-b36-SourceStrand.zip
Human610-Quadv1_B-b37-SourceStrand.zip

Human610-Quadv1_H
human610-quadv1_h-b35-strand.zip
human610-quadv1_h-b36-strand.zip
human610-quadv1_h-b37-strand.zip
human610-quadv1_h-b38-strand.zip

HumanHap650Yv3_A
HumanHap650Yv3_A-b35-strand.zip
HumanHap650Yv3_A-b36-strand.zip
HumanHap650Yv3_A-b37-strand.zip
HumanHap650Yv3_A-b38-strand.zip
Source Strand Versions
HumanHap650Yv3_A-b36-SourceStrand.zip
HumanHap650Yv3_A-b37-SourceStrand.zip

Human660W-Quad_v1_A
Human660W-Quad_v1_A-b35.strand.zip
Human660W-Quad_v1_A-b36.strand.zip
Human660W-Quad_v1_A-b37.strand.zip
Human660W-Quad_v1_A-b38.strand.zip

Human660W-Quad_v1_C
Human660W-Quad_v1_C-b35.zip
Human660W-Quad_v1_C-b36.zip
Human660W-Quad_v1_C-b37.zip
Human660W-Quad_v1_C-b38.zip

Human660W-Quadv1_H
human660w-quad_v1_h-b35-strand.zip
human660w-quad_v1_h-b36-strand.zip
human660w-quad_v1_h-b37-strand.zip
human660w-quad_v1_h-b38-strand.zip

Human670-QuadCustom_v1_A
Human670-QuadCustom_v1_A-b35-strand.zip
Human670-QuadCustom_v1_A-b36-strand.zip
Human670-QuadCustom_v1_A-b37-strand.zip
Human670-QuadCustom_v1_A-b38-strand.zip

HumanOmniExpress-12v1_A
HumanOmniExpress-12v1_A-b35-strand.zip
HumanOmniExpress-12v1_A-b36v2-strand.zip
HumanOmniExpress-12v1_A-b37-strand.zip
HumanOmniExpress-12v1_A-b38-strand.zip
HumanOmniExpress12v1_A AB to TOP alleles Mapping
HumanOmniExpress-12v1_A.update_alleles.txt.gz
Zip version for those with problems downloading the gzip version above
HumanOmniExpress-12v1_A.update_alleles.txt.zip

HumanOmniExpress-12v1-1_A
HumanOmniExpress-12v1-1_A-b35-strand.zip
HumanOmniExpress-12v1-1_A-b36-strand.zip
HumanOmniExpress-12v1-1_A-b37-strand.zip
HumanOmniExpress-12v1-1_A-b38-strand.zip

HumanOmniExpress-12v1_B
HumanOmniExpress-12v1-Multi_B-b35-strand.zip
HumanOmniExpress-12v1-Multi_B-b36-strand.zip
HumanOmniExpress-12v1-Multi_B-b37-strand.zip
HumanOmniExpress-12v1-Multi_B-b38-strand.zip

HumanOmniExpress-12v1-1_B
HumanOmniExpress-12v1-1_B-b35-strand.zip
HumanOmniExpress-12v1-1_B-b36-strand.zip
HumanOmniExpress-12v1-1_B-b37-strand.zip
HumanOmniExpress-12v1-1_B-b38-strand.zip

HumanOmniExpress-12v1_C
HumanOmniExpress-12v1-Multi_C-b35-strand.zip
HumanOmniExpress-12v1-Multi_C-b36-strand.zip
HumanOmniExpress-12v1-Multi_C-b37-strand.zip
HumanOmniExpress-12v1-Multi_C-b38-strand.zip

HumanOmniExpress-12v1_H
HumanOmniExpress-12v1_H-b35-strand.zip
HumanOmniExpress-12v1_H-b36-strand.zip
HumanOmniExpress-12v1_H-b37.strand.zip
HumanOmniExpress-12v1_H-b38-strand.zip

HumanOmniExpress-12v1_J
HumanOmniExpress-12v1_J-b35-strand.zip
HumanOmniExpress-12v1_J-b36-strand.zip
HumanOmniExpress-12v1_J-b37.strand.zip
HumanOmniExpress-12v1_J-b38-strand.zip

HumanOmniExpress-12v1_J_FFPE
HumanOmniExpress-12v1_J_FFPE-b35-strand.zip
HumanOmniExpress-12v1_J_FFPE-b36-strand.zip
HumanOmniExpress-12v1_J_FFPE-b37-strand.zip
HumanOmniExpress-12v1_J_FFPE-b38-strand.zip

humanomniexpress-24v1-0_a
humanomniexpress-24v1-0_a-b35-strand.zip
humanomniexpress-24v1-0_a-b36-strand.zip
humanomniexpress-24v1-0_a-b37-strand.zip
humanomniexpress-24v1-0_a-b38-strand.zip

humanomniexpress-24v1-1-a
humanomniexpress-24-v1-1-a-b35-strand.zip
humanomniexpress-24-v1-1-a-b36-strand.zip
humanomniexpress-24-v1-1-a-b37-strand.zip
humanomniexpress-24-v1-1-a-b38-strand.zip

HumanOmniExpress-24-v1-0-B
HumanOmniExpress-24-v1-0-B-b35-strand.zip
HumanOmniExpress-24-v1-0-B-b36-strand.zip
HumanOmniExpress-24-v1-0-B-b37-strand.zip
HumanOmniExpress-24-v1-0-B-b38-strand.zip

InfiniumOmniExpress-24v1-2_A1
InfiniumOmniExpress-24v1-2_A1-b35-strand.zip
InfiniumOmniExpress-24v1-2_A1-b36-strand.zip
InfiniumOmniExpress-24v1-2_A1-b37-strand.zip
InfiniumOmniExpress-24v1-2_A1-b38-strand.zip

HumanOmniExpressExome-8v1_A
HumanOmniExpressExome-8v1_A-b35-strand.zip
HumanOmniExpressExome-8v1_A-b36-strand.zip
HumanOmniExpressExome-8v1_A-b37.strand.zip
HumanOmniExpressExome-8v1_A-b38-strand.zip

humanomniexpressexome-8v1-0_a
humanomniexpressexome-8v1-0_a-b35-strand.zip
humanomniexpressexome-8v1-0_a-b36-strand.zip
humanomniexpressexome-8v1-0_a-b37-strand.zip
humanomniexpressexome-8v1-0_a-b38-strand.zip

HumanOmniExpressExome-8-v1-0-B
HumanOmniExpressExome-8-v1-0-B-b35-strand.zip
HumanOmniExpressExome-8-v1-0-B-b36-strand.zip
HumanOmniExpressExome-8-v1-0-B-b37-strand.zip
HumanOmniExpressExome-8-v1-0-B-b38-strand.zip

HumanOmniExpressExome-8v1-2_A
HumanOmniExpressExome-8v1-2_A-b35-strand.zip
HumanOmniExpressExome-8v1-2_A-b36-strand.zip
HumanOmniExpressExome-8v1-2_A-b37-strand.zip
HumanOmniExpressExome-8v1-2_A-b38-strand.zip
 HumanOmniExpressExome-8v1-2_A Source Strand Versions
HumanOmniExpressExome-8v1-2_A-b35-Source.zip
HumanOmniExpressExome-8v1-2_A-b36-Source.zip
HumanOmniExpressExome-8v1-2_A-b37-Source.zip
HumanOmniExpressExome-8v1-2_A-b38-Source.zip

HumanOmniExpressExome-8-v1-2-B
HumanOmniExpressExome-8-v1-2-B-b35-strand.zip
HumanOmniExpressExome-8-v1-2-B-b36-strand.zip
HumanOmniExpressExome-8-v1-2-B-b37-strand.zip
HumanOmniExpressExome-8-v1-2-B-b38-strand.zip

OmniExpressExome-8v1-1_A
OmniExpressExome-8v1-1_A-b35-strand.zip
OmniExpressExome-8v1-1_A-b36-strand.zip
OmniExpressExome-8v1-1_A-b37-strand.zip
OmniExpressExome-8v1-1_A-b38-strand.zip

OmniExpressExome-8v1-1_B
OmniExpressExome-8v1-1_B-b35-strand.zip
OmniExpressExome-8v1-1_B-b36-strand.zip
OmniExpressExome-8v1-1_B-b37-strand.zip
OmniExpressExome-8v1-1_B-b38-strand.zip

InfiniumOmniExpressExome-8v1-3_A
InfiniumOmniExpressExome-8v1-3_A-b35-strand.zip
InfiniumOmniExpressExome-8v1-3_A-b36-strand.zip
InfiniumOmniExpressExome-8v1-3_A-b37-strand.zip
InfiniumOmniExpressExome-8v1-3_A-b38-strand.zip

InfiniumOmniExpressExome-8v1-4_A1
InfiniumOmniExpressExome-8v1-4_A1-b35-strand.zip
InfiniumOmniExpressExome-8v1-4_A1-b36-strand.zip
InfiniumOmniExpressExome-8v1-4_A1-b37-strand.zip
InfiniumOmniExpressExome-8v1-4_A1-b38-strand.zip

HumanOmni25Exome-8v1_A
HumanOmni25Exome-8v1_A-b35-strand.zip
HumanOmni25Exome-8v1_A-b36-strand.zip
HumanOmni25Exome-8v1_A-b37-strand.zip
HumanOmni25Exome-8v1_A-b38-strand.zip

HumanOmni2-5Exome-8-v1-1-A
HumanOmni2-5Exome-8-v1-1-A-b35-strand.zip
HumanOmni2-5Exome-8-v1-1-A-b36-strand.zip
HumanOmni2-5Exome-8-v1-1-A-b37-strand.zip
HumanOmni2-5Exome-8-v1-1-A-b38-strand.zip

InfiniumOmni2.5Exome-8v1-2_A
InfiniumOmni2.5Exome-8v1-2_A-b35-strand.zip
InfiniumOmni2.5Exome-8v1-2_A-b36-strand.zip
InfiniumOmni2.5Exome-8v1-2_A-b37-strand.zip
InfiniumOmni2.5Exome-8v1-2_A-b38-strand.zip

InfiniumOmni2-5Exome-8v1-3_A1
InfiniumOmni2-5Exome-8v1-3_A1-b35-strand.zip
InfiniumOmni2-5Exome-8v1-3_A1-b36-strand.zip
InfiniumOmni2-5Exome-8v1-3_A1-b37-strand.zip
InfiniumOmni2-5Exome-8v1-3_A1-b38-strand.zip

HumanOmniZhongHua-8v1_B
HumanOmniZhongHua-8v1_B-b35-strand.zip
HumanOmniZhongHua-8v1_B-b36.strand.zip
HumanOmniZhongHua-8v1_B-b37.strand.zip
HumanOmniZhongHua-8v1_B-b38-strand.zip

HumanOmniZhongHua-8v1-1_A
humanomnizhonghua-8v1-1_a-b35-strand.zip
humanomnizhonghua-8v1-1_a-b36-strand.zip
humanomnizhonghua-8v1-1_a-b37-strand.zip
humanomnizhonghua-8v1-1_a-b38-strand.zip

HumanOmniZhongHua-8v1-2_A
HumanOmniZhongHua-8v1-2_A-b35-strand.zip
HumanOmniZhongHua-8v1-2_A-b36-strand.zip
HumanOmniZhongHua-8v1-2_A-b37-strand.zip
HumanOmniZhongHua-8v1-2_A-b38-strand.zip

InfiniumOmniZhongHua-8v1-3_A
InfiniumOmniZhongHua-8v1-3_A1-b35-strand.zip
InfiniumOmniZhongHua-8v1-3_A1-b36-strand.zip
InfiniumOmniZhongHua-8v1-3_A1-b37-strand.zip
InfiniumOmniZhongHua-8v1-3_A1-b38-strand.zip

Human1Mv1_C
Human1Mv1_C-b35-strand.zip
Human1Mv1_C-b36-strand.zip
Human1Mv1_C-b37-strand.zip
Human1Mv1_C-b38-strand.zip

Human1M-Duov3_B
Human1M-Duov3_B-b35-strand.zip
Human1M-Duov3_B-b36-strand.zip
Human1MDuo-b37-strand-v2.zip
Updated versions with INDEL alleles corrected
Human1M-Duov3_B-b37-strand.zip
Human1M-Duov3_B-b38-strand.zip

Human1M-Duov3_C
Human1MDuov3_C-b37-strand.zip
Updated versions with INDEL alleles corrected
Human1M-Duov3_C-b35-strand.zip
Human1M-Duov3_C-b36-strand.zip
Human1M-Duov3_C-b37-strand.zip
Human1M-Duov3_C-b38-strand.zip

human1m-duov3_h
human1m-duov3_h-b35-strand.zip
human1m-duov3_h-b36-strand.zip
human1m-duov3_h-b37-strand.zip
human1m-duov3_h-b38-strand.zip

HumanOmni1-Quad_v1-0_B
HumanOmni1-Quad_v1-0_B-b35.strand.zip
HumanOmni1-Quad_v1-0_B-b36-strand.zip
HumanOmni1-Quad_v1-0_B-b37.strand.zip
HumanOmni1-Quad_v1-0_B-b38.strand.zip
HumanOmni1-Quad_v1-0_B Source Strand Versions
HumanOmni1-Quad_v1-0_B-b36-SOURCE.strand.zip
HumanOmni1-Quad_v1-0_B-b37-SOURCE.strand.zip

HumanOmni1-Quad_v1-0_C
HumanOmni1-Quad_v1-0_C-b35-strand.zip
HumanOmni1-Quad_v1-0_C-b36-strand.zip
HumanOmni1-Quad_v1-0_C-b37-strand.zip
HumanOmni1-Quad_v1-0_C-b38-strand.zip

HumanOmni1-Quad_v1-0_H
HumanOmni1-Quad_v1-0_H-b35-strand.zip
HumanOmni1-Quad_v1-0_H-b36-strand.zip
HumanOmni1-Quad_v1-0_H-b37-strand.zip
HumanOmni1-Quad_v1-0_H-b38-strand.zip

humanomni1-quad_v1-0-multi_h
humanomni1-quad_v1-0-multi_h-b35-strand.zip
humanomni1-quad_v1-0-multi_h-b36-strand.zip
humanomni1-quad_v1-0-multi_h-b37-strand.zip
humanomni1-quad_v1-0-multi_h-b38-strand.zip

HumanOmni1S-8v1_H
HumanOmni1S-8v1_H-b35-strand.zip
HumanOmni1S-8v1_H-b36-strand.zip
HumanOmni1S-8v1_H-b37-strand.zip
HumanOmni1S-8v1_H-b38-strand.zip

Human1.2MDuoCustom_v1_A
Human1-2M-DuoCustom_v1_A-b35-strand.zip
Human1-2M-DuoCustom_v1_A-b36-strand.zip
Human1-2M-DuoCustom_v1_A-b37-strand.zip
Human1-2M-DuoCustom_v1_A-b38-strand.zip

HumanOmni2.5-4v1_B
HumanOmni2.5-4v1_B-b35-strand.zip
HumanOmni2.5M-b36-strand.zip
HumanOmni2.5M-b37-strand-v2.zip
HumanOmni2.5-4v1_B-b38-strand.zip

HumanOmni2.5-4v1_D
HumanOmni2.5-4v1_D-b35-strand.zip
HumanOmni2.5-4v1_D-b36-strand.zip
HumanOmni2.5-4v1_D-b37-strand.zip
HumanOmni2.5-4v1_D-b38-strand.zip

HumanOmni2.5-4v1_H
HumanOmni2.5-4v1_H-b35-strand.zip
HumanOmni2.5-4v1_H-b36-strand.zip
HumanOmni2.5-4v1_H-b37-strand.zip
HumanOmni2.5-4v1_H-b38-strand.zip

HumanOmni2.5-8v1_A
HumanOmni2.5-8v1_A-b35-strand.zip
HumanOmni2.5-8v1_A-b36-strand.zip
HumanOmni2.5-8v1_A-b37-strand.zip
HumanOmni2.5-8v1_A-b38-strand.zip
Source Strand Versions
HumanOmni2.5-8v1_A-b35-Source.strand.zip
HumanOmni2.5-8v1_A-b36-Source.strand.zip
HumanOmni2.5-8v1_A-b37-Source.strand.zip
HumanOmni2.5-8v1_A-b38-Source.strand.zip

HumanOmni2.5-8v1-0-D
HumanOmni2-5-8-v1-0-D-b35-strand.zip
HumanOmni2-5-8-v1-0-D-b36-strand.zip
HumanOmni2-5-8-v1-0-D-b37-strand.zip
HumanOmni2-5-8-v1-0-D-b38-strand.zip

HumanOmni25-8v1-1_A
HumanOmni25-8v1-1_A-b35-strand.zip
HumanOmni25-8v1-1_A-b36-strand.zip
HumanOmni25-8v1-1_A-b37-strand.zip
HumanOmni25-8v1-1_A-b38-strand.zip

HumanOmni2-5-8-v1-2-A
HumanOmni2-5-8-v1-2-A-b35-strand.zip
HumanOmni2-5-8-v1-2-A-b36-strand.zip
HumanOmni2-5-8-v1-2-A-b37-strand.zip
HumanOmni2-5-8-v1-2-A-b38-strand.zip

humanomni25m-8v1-1_b
humanomni25m-8v1-1_b-b35-strand.zip
humanomni25m-8v1-1_b-b36-strand.zip
humanomni25m-8v1-1_b-b37-strand.zip
humanomni25m-8v1-1_b-b38-strand.zip

HumanOmni2.5-8v1_C
HumanOmni2.5-8v1_C-b35-strand.zip
HumanOmni2.5-8v1_C-b36-strand.zip
HumanOmni2.5-8v1_C-b37-strand.zip
HumanOmni2.5-8v1_C-b38-strand.zip

HumanOmni2.5-8v1-1-C
HumanOmni2-5-8-v1-1-C-b35-strand.zip
HumanOmni2-5-8-v1-1-C-b36-strand.zip
HumanOmni2-5-8-v1-1-C-b37-strand.zip
HumanOmni2-5-8-v1-1-C-b38-strand.zip

HumanOmni2.5S-8v1_B
HumanOmni2.5S-8v1_B-b35-strand.zip
HumanOmni2.5S-8v1_B-b36-strand.zip
HumanOmni2.5S-8v1_B-b37-strand.zip
HumanOmni2.5S-8v1_B-b38-strand.zip

HumanOmni25-8v1-2_A1
HumanOmni25-8v1-2_A1-b35-strand.zip
HumanOmni25-8v1-2_A1-b36-strand.zip
HumanOmni25-8v1-2_A1-b37-strand.zip
HumanOmni25-8v1-2_A1-b38-strand.zip

InfiniumOmni2-5-8v1-3_A1
InfiniumOmni2-5-8v1-3_A1-b35-strand.zip
InfiniumOmni2-5-8v1-3_A1-b36-strand.zip
InfiniumOmni2-5-8v1-3_A1-b37-strand.zip
InfiniumOmni2-5-8v1-3_A1-b38-strand.zip

HumanOmni5-4v1_B
HumanOmni5-4v1_B-b35-strand.zip
HumanOmni5-4v1_B-b36-strand.zip
HumanOmni5-4v1_B-b37-strand.zip
HumanOmni5-4v1_B-b38-strand.zip

humanomni5-4v1_c
humanomni5-4v1_c-b35-strand.zip
HumanOmni5-4v1_C-b36-strand.zip
humanomni5-4v1_c-b37-strand.zip
HumanOmni5-4v1_C-b38-strand.zip

HumanOmni5-4-v1-0-D
HumanOmni5-4-v1-0-D-b35-strand.zip
HumanOmni5-4-v1-0-D-b36-strand.zip
HumanOmni5-4-v1-0-D-b37-strand.zip
HumanOmni5-4-v1-0-D-b38-strand.zip

HumanOmni5-4v1-1_A
HumanOmni5-4v1-1_A-b35-strand.zip
HumanOmni5-4v1-1_A-b36-strand.zip
HumanOmni5-4v1-1_A-b37-strand.zip
HumanOmni5-4v1-1_A-b38-strand.zip

HumanOmni5Exome-4v1_A
HumanOmni5Exome-4v1_A-b35-strand.zip
humanomni5exome-4v1_a-b36-strand.zip
HumanOmni5Exome-4v1_A-b37-strand.zip
humanomni5exome-4v1_a-b38-strand.zip

HumanOmni5Exome-4v1-1_A
HumanOmni5Exome-4v1-1_A-b35-strand.zip
HumanOmni5Exome-4v1-1_A-b36-strand.zip
HumanOmni5Exome-4v1-1_A-b37-strand.zip
HumanOmni5Exome-4v1-1_A-b38-strand.zip
Source Strand
HumanOmni5Exome-4v1-1_A-b35-Source.strand.zip
HumanOmni5Exome-4v1-1_A-b36-Source.strand.zip
HumanOmni5Exome-4v1-1_A-b37-Source.strand.zip
HumanOmni5Exome-4v1-1_A-b38-Source.strand.zip

HumanOmni5Exome-4v1-2_A
HumanOmni5Exome-4v1-2_A-b35-strand.zip
HumanOmni5Exome-4v1-2_A-b36-strand.zip
HumanOmni5Exome-4v1-2_A-b37-strand.zip
HumanOmni5Exome-4v1-2_A-b38-strand.zip

HumanCytoSNP-12v1-0_D
HumanCytoSNP-12v1-0_D-b35-strand.zip
HumanCytoSNP-12v1-0_D-b36-strand.zip
HumanCytoSNP-12v1-0_D-b37-strand.zip
HumanCytoSNP-12v1-0_D-b38-strand.zip

HumanCytoSNP-12v2.1-FFPE_G
HumanCytoSNP-12v2.1-FFPE_G-b35-strand.zip
HumanCytoSNP-12v2.1-FFPE_G-b36-strand.zip
HumanCytoSNP-12v2.1-FFPE_G-b37-strand.zip
HumanCytoSNP-12v2.1-FFPE_G-b38-strand.zip

HumanCytoSNP-12v2_H
humancytosnp-12v2_h-b35-strand.zip
humancytosnp-12v2_h-b36-strand.zip
humancytosnp-12v2_h-b37-strand.zip
humancytosnp-12v2_h-b38-strand.zip

HumanCytoSNP-12v2-1_H
humancytosnp-12v2-1_h-b35-strand.zip
humancytosnp-12v2-1_h-b36-strand.zip
humancytosnp-12v2-1_h-b37-strand.zip
humancytosnp-12v2-1_h-b38-strand.zip
HumanCytoSNP-12v2-1_H Source Strand Versions
humancytosnp-12v2-1_h-b35.source.zip
humancytosnp-12v2-1_h-b36.source.zip
humancytosnp-12v2-1_h-b37.source.zip
humancytosnp-12v2-1_h-b38.source.zip

HumanCytoSNP-12v2-1_L
humancytosnp-12v2-1_l-b35-strand.zip
humancytosnp-12v2-1_l-b36-strand.zip
humancytosnp-12v2-1_l-b37-strand.zip
humancytosnp-12v2-1_l-b38-strand.zip
HumanCytoSNP-12v2-1_L Source Strand Versions
humancytosnp-12v2-1_l-b35.source.zip
humancytosnp-12v2-1_l-b36.source.zip
humancytosnp-12v2-1_l-b37.source.zip
humancytosnp-12v2-1_l-b38.source.zip

cytosnp-850k_b
cytosnp-850k_b-b35-strand.zip
cytosnp-850k_b-b36-strand.zip
cytosnp-850k_b-b37-strand.zip
cytosnp-850k_b-b38-strand.zip

CytoSNP-850K_v1-1
CytoSNP-850K_v1-1_iScan_A1-b35-strand.zip
CytoSNP-850K_v1-1_iScan_A1-b36-strand.zip
CytoSNP-850K_v1-1_iScan_A1-b37-strand.zip
CytoSNP-850K_v1-1_iScan_A1-b38-strand.zip

HumanCore-12v1-0_A
humancore-12v1-0_a-b35-strand.zip
humancore-12v1-0_a-b36-strand.zip
humancore-12v1-0_a-b37-strand.zip
Updated Versions with INDEL alleles corrected
humancore-12v1-0_a-b35-strand-v2.zip
humancore-12v1-0_a-b36-strand-v2.zip
humancore-12v1-0_a-b37-strand-v2.zip
humancore-12v1-0_a-b38-strand-v2.zip

HumanCore-12-v1-0-B
HumanCore-12-v1-0-B-b35-strand.zip
HumanCore-12-v1-0-B-b36-strand.zip
HumanCore-12-v1-0-B-b37-strand.zip
HumanCore-12-v1-0-B-b38-strand.zip

HumanCore-24-v1-0_A
humancore-24-v1-0-manifest-file-a-b35-strand.zip
humancore-24-v1-0-manifest-file-a-b36-strand.zip
humancore-24-v1-0-manifest-file-a-b37-strand.zip
humancore-24-v1-0-manifest-file-a-b38-strand.zip

Immuno_BeadChip_11419691_B
Immuno_BeadChip_11419691_B-b35-strand.zip
Immuno_BeadChip_11419691_B-b36-strand.zip
Immuno_BeadChip_11419691_B-b37-strand.zip
Immuno_BeadChip_11419691_B-b38-strand.zip

InfiniumImmunoArray-24v2-0_A
InfiniumImmunoArray-24v2-0_A-b35-strand.zip
InfiniumImmunoArray-24v2-0_A-b36-strand.zip
InfiniumImmunoArray-24v2-0_A-b37-strand.zip
InfiniumImmunoArray-24v2-0_A-b38-strand.zip

Multi-EthnicGlobal_A1
Multi-EthnicGlobal_A1-b35-strand.zip
Multi-EthnicGlobal_A1-b36-strand.zip
Multi-EthnicGlobal_A1-b37-strand.zip
Multi-EthnicGlobal_A1-b38-strand.zip

HumanExome-12v1_A
HumanExome-12v1_A-b35-strand.zip
HumanExome-12v1_A-b36-strand.zip
HumanExome-12v1_A-b37-strand.zip
HumanExome-12v1_A-b38-strand.zip
HumanExome-12v1_A AB to TOP alleles Mapping
HumanExome.A.update_alleles.txt.gz
Zip version for those with problems downloading the gzip version above
HumanExome-12v1_A.update_alleles.txt.zip

HumanExome-12v1-1_A
HumanExome-12v1-1_A-b35-strand.zip
HumanExome-12v1-1_A-b36-strand.zip
HumanExome-12v1-1_A-b37-strand.zip
HumanExome-12v1-1_A-b38-strand.zip
Source Strand versions
HumanExome-12v1-1_A-b36-SourceStrand.zip
HumanExome-12v1-1_A-b37-SourceStrand.zip

HumanExome-12v1-2_A
HumanExome-12v1-2_A-b35-strand.zip
HumanExome-12v1-2_A-b36-strand.zip
HumanExome-12v1-2_A-b37-strand.zip
HumanExome-12v1-2_A-b38-strand.zip

HumanCoreExome-12v1-0_B
HumanCoreExome-12v1-0_B-b35-strand.zip
HumanCoreExome-12v1-0_B-b36.strand.zip
HumanCoreExome-12v1-0_B-b37.strand.zip
HumanCoreExome-12v1-0_B-b38-strand.zip
ILLM Strand Version
HumanCoreExome-12v1-0_B-b37-ILLM.zip

HumanCoreExome-12v1-0_C
humancoreexome-12v1-0_c-b35-strand.zip
humancoreexome-12v1-0_c-b36-strand.zip
humancoreexome-12v1-0_c-b37-strand.zip
humancoreexome-12v1-0_c-b38-strand.zip

HumanCoreExome-12v1-0-D
HumanCoreExome-12-v1-0-D-b35-strand.zip
HumanCoreExome-12-v1-0-D-b36-strand.zip
HumanCoreExome-12-v1-0-D-b37-strand.zip
HumanCoreExome-12-v1-0-D-b38-strand.zip

HumanCoreExome-12v1-1_A
humancoreexome-12v1-1_a-b35-strand.zip
humancoreexome-12v1-1_a-b36-strand.zip
humancoreexome-12v1-1_a-b37-strand.zip
humancoreexome-12v1-1_a-b38-strand.zip

HumanCoreExome-12v1-1_B
HumanCoreExome-12v1-1_B-b35-strand.zip
HumanCoreExome-12v1-1_B-b36-strand.zip
HumanCoreExome-12v1-1_B-b37-strand.zip
HumanCoreExome-12v1-1_B-b38-strand.zip

HumanCoreExome-12v1-1-C
HumanCoreExome-12-v1-1-C-b35-strand.zip
HumanCoreExome-12-v1-1-C-b36-strand.zip
HumanCoreExome-12-v1-1-C-b37-strand.zip
HumanCoreExome-12-v1-1-C-b38-strand.zip

HumanCoreExome-24v1-0_A
HumanCoreExome-24v1-0_A-b35-strand.zip
HumanCoreExome-24v1-0_A-b36-strand.zip
HumanCoreExome-24v1-0_A-b37-strand.zip
HumanCoreExome-24v1-0_A-b38-strand.zip

InfiniumCoreExome-24v1-1_A
InfiniumCoreExome-24v1-1_A-b35-strand.zip
InfiniumCoreExome-24v1-1_A-b36-strand.zip
InfiniumCoreExome-24v1-1_A-b37-strand.zip
InfiniumCoreExome-24v1-1_A-b38-strand.zip

Cardio-Metabo_Chip_11395247_A
Metabochip-strand-b36-v5.zip
Metabochip-b37.58-v2.zip
Cardio-Metabo_Chip_11395247_A Source Strand version
Metabochip-b36-v5-SourceStrand.zip
Metabochip-b37-SourceStrand.zip

Cardio-Metabo_Chip_11395247_A Allele sets
Metabochip-alleles.zip

cardio-metabo_chip_11395247_C
cardio-metabo_chip_11395247_c-b35-strand.zip
cardio-metabo_chip_11395247_c-b36-strand.zip
cardio-metabo_chip_11395247_c-b37-strand.zip
cardio-metabo_chip_11395247_c-b38-strand.zip

CVDSNP55v1_A
CVDSNP55v1_A-b35-strand.zip
CVDSNP55v1_A-b36-strand.zip
CVDSNP55v1_A-b37-strand.zip
CVDSNP55v1_A-b38-strand.zip

PsychArray_A
PsychArray_A-b35-strand.zip
PsychArray_A-b36-strand.zip
PsychArray_A-b37-strand.zip
PsychArray_A-b38-strand.zip

PsychArray_B
PsychArray-B-b35-strand.zip
PsychArray-B-b36-strand.zip
PsychArray-B-b37-strand.zip
PsychArray-B-b38-strand.zip

InfiniumPsychArray-24v1-1_A1
InfiniumPsychArray-24v1-1_A1-b35-strand.zip
InfiniumPsychArray-24v1-1_A1-b36-strand.zip
InfiniumPsychArray-24v1-1_A1-b37-strand.zip
InfiniumPsychArray-24v1-1_A1-b38-strand.zip

PsychChip_15048346_B
PsychChip_15048346_B-b35-strand.zip
PsychChip_15048346_B-b36-strand.zip
PsychChip_15048346_B-b37-strand.zip
PsychChip_15048346_B-b38-strand.zip

PsychChip_v1-1_15073391_A
PsychChip_v1-1_15073391_A1-b35-strand.zip
PsychChip_v1-1_15073391_A1-b36-strand.zip
PsychChip_v1-1_15073391_A1-b37-strand.zip
PsychChip_v1-1_15073391_A1-b38-strand.zip

Affymetrix data files
The Affymetrix zip files contain only the strand file and the file has five columns SNP id, chromosome, position, %match to genome and strand. The IDs used are the Affymetrix SNP_A ids to avoid issues with changes to SNP rs ids between builds.

Affy 500K (Nsp and Sty Chips)
Affy-NSP-STY-b37.58-v4.zip

Affymetrix 6.0 (1M chip)
GenomeWide_6-b37.58-v2.zip

Strand and position derived from the Affymetrix releases

Affy 500K (Nsp and Sty Chips)
Nsp-Sty.na31-b37-strand.zip
Nsp-Sty.na30-b36-strand.zip

Affymetrix 6.0 (1M chip)
GenomeWideSNP_6.na30-b36-strand.zip
GenomewideSNP_6.na31-b37-strand.zip
GenomeWideSNP_6.na32-b37.strand.zip

50K_Xba240
50K_Xba240.na32.strand.zip