Genotyping chips strand and build files

This page contains files giving the strand orientation and position of variants of the most common genotyping chips on genome builds 36 to 38 inclusive. New files will be added as new genome builds are released

Note: Genome build 35 links have now been removed from all the pages. The files are though still available and are still created by default for all new chips, in the event you require one of these files please email me

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 post the file to this page.



Illumina data files

The data for each chip and genome build combination are freely downloadable from the links below, each zip file contains three files, these are:
.strand file
.miss file
.multiple file

.strand file This contains all the variants where the match to the relevant genomic sequence >90%. The strand file contains six columns, SNP id, chromosome, position, %match to genome, strand and TOP alleles. The SNP ids used are those from the Illumina annotation file and so are not necessarily the latest ones for that position 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 your 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 by exporting on a different strand, such as ILMN or SOURCE in this case please check the links in the menu above to those pages. If that is still unsuccessful then if you can provide a list of the SNP ids and their alleles on the chip (a plink .bim file is ideal for this) it is likely a strand file can be created for you.

.miss file 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.

.multiple file 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 number of these is reported, this is first numeric column in the file. If there are two matches of the same quality then one is chosen at random and the number of identical matches is reported, this is the second numeric column in the file.

Other Allele Sets

The strand files on this page assume that your genotype calling algorithm has exported the allele calls aligned to the Illumina TOP strand, if this is not the case for your data file then the most likely alternative is using the alleles derived from the Source Sequence in the annotation file. There are a few of these files on this page, and these will remain as is, however the best and most up to date resource for the alternative strand information is to use the
Source Strand Files and Ilmn Strand Files links from the menu above.

Updating the strand and position

A script developed by Neil Robertson for updating the chromosome, 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, ILMN)
<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 work can be downloaded here:
WR-ASHG2011posterPP-portrait.pdf

Allele Updates

If your genotype calls are represented as A/B then the files present here allow you to update the alleles from A/B to TOP strand A, C, G, T calls suitable for use with the stran files on this page, if the chip you are using is not listed contact me and I can create these files.

Ref/Alt

Files listing the Reference and Alternate alleles 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
BDCHP-1X10-HUMANHAP240S_11216501_A-b38-strand.zip

HumanHap300v1-1_11219278_C
BDCHP-1x10-HUMANHAP300v1-1_11219278_C-b36-strand.zip
BDCHP-1x10-HUMANHAP300v1-1_11219278_C-b37-strand.zip
BDCHP-1x10-HUMANHAP300v1-1_11219278_C-b38-strand.zip
HumanHap300v1-1_11219278_C Source Strand Versions
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
HumanHap300v2_A-b38-strand.zip

Human CNV370v1_C
HumanCNV370v1_C-b36-strand.zip
HumanCNV370v1_C-b37-strand.zip
HumanCNV370v1_C-b38-strand.zip
Human CNV370v1_C Source Strand Versions
HumanCNV370v1_C-b36-SourceStrand.zip
HumanCNV370v1_C-b37-SourceStrand.zip

HumanCNV370-Quadv3_C
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
BDCHP-1X10-HUMANHAP550_11218540_C-b38-strand.zip

HumanHap550-2v3_B
HumanHap550-2v3_B-b36-strand.zip
HumanHap550-2v3_B-b37-strand.zip
HumanHap550-2v3_B-b38-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-b36-strand.zip
HumanHap550v3_A-b37-strand.zip
HumanHap550v3_A-b38-strand.zip

Human610Quadv1_B
Human610-Quadv1_B-b36-strand.zip
Human610-Quadv1_B-b37-strand.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-b36-strand.zip
human610-quadv1_h-b37-strand.zip
human610-quadv1_h-b38-strand.zip

HumanHap650Yv3_A
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-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-b36.zip
Human660W-Quad_v1_C-b37.zip
Human660W-Quad_v1_C-b38.zip

Human660W-Quadv1_H
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-b36-strand.zip
Human670-QuadCustom_v1_A-b37-strand.zip
Human670-QuadCustom_v1_A-b38-strand.zip

HumanOmniExpress-12v1_A
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-b36-strand.zip
HumanOmniExpress-12v1-1_A-b37-strand.zip
HumanOmniExpress-12v1-1_A-b38-strand.zip

HumanOmniExpress-12v1_B
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-b36-strand.zip
HumanOmniExpress-12v1-1_B-b37-strand.zip
HumanOmniExpress-12v1-1_B-b38-strand.zip

HumanOmniExpress-12v1_C
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-b36-strand.zip
HumanOmniExpress-12v1_H-b37-strand.zip
HumanOmniExpress-12v1_H-b38-strand.zip

HumanOmniExpress-12v1_J
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-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-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-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-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-b36-strand.zip
InfiniumOmniExpress-24v1-2_A1-b37-strand.zip
InfiniumOmniExpress-24v1-2_A1-b38-strand.zip

HumanOmniExpressExome-8v1_A
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-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-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-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-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-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-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-b36-strand.zip
OmniExpressExome-8v1-1_B-b37-strand.zip
OmniExpressExome-8v1-1_B-b38-strand.zip

HumanOmniExpressExome-8-v1-1-C
HumanOmniExpressExome-8-v1-1-C-b36-strand.zip
HumanOmniExpressExome-8-v1-1-C-b37-strand.zip
HumanOmniExpressExome-8-v1-1-C-b38-strand.zip

InfiniumOmniExpressExome-8v1-3_A
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-b36-strand.zip
InfiniumOmniExpressExome-8v1-4_A1-b37-strand.zip
InfiniumOmniExpressExome-8v1-4_A1-b38-strand.zip

HumanOmni25Exome-8v1_A
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-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-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-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-b36-strand.zip
HumanOmniZhongHua-8v1_B-b37-strand.zip
HumanOmniZhongHua-8v1_B-b38-strand.zip

HumanOmniZhongHua-8v1-1_A
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-b36-strand.zip
HumanOmniZhongHua-8v1-2_A-b37-strand.zip
HumanOmniZhongHua-8v1-2_A-b38-strand.zip

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

InfiniumOmniZhongHua-8v1-3_A2
InfiniumOmniZhongHua-8v1-3_A2-b36-strand.zip
InfiniumOmniZhongHua-8v1-3_A2-b37-strand.zip
InfiniumOmniZhongHua-8v1-3_A2-b38-strand.zip
Human1Mv1_C
Human1Mv1_C-b36-strand.zip
Human1Mv1_C-b37-strand.zip
Human1Mv1_C-b38-strand.zip

Human1M-Duov3_B
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-b36-strand.zip
Human1M-Duov3_C-b37-strand.zip
Human1M-Duov3_C-b38-strand.zip

human1m-duov3_h
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-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-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-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-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-b36-strand.zip
HumanOmni1S-8v1_H-b37-strand.zip
HumanOmni1S-8v1_H-b38-strand.zip

Human1.2MDuoCustom_v1_A
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-b36-strand.zip
HumanOmni2.5-4v1_B-b37-strand.zip
HumanOmni2.5-4v1_B-b38-strand.zip

HumanOmni2.5-4v1_D
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-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-b36-strand.zip
HumanOmni2.5-8v1_A-b37-strand.zip
HumanOmni2.5-8v1_A-b38-strand.zip
Source Strand Versions
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-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-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-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-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-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-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-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-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-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-b36-strand.zip
HumanOmni5-4v1_B-b37-strand.zip
HumanOmni5-4v1_B-b38-strand.zip

humanomni5-4v1_c
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-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-b36-strand.zip
HumanOmni5-4v1-1_A-b37-strand.zip
HumanOmni5-4v1-1_A-b38-strand.zip

InfiniumOmni5-4v1-2_A1
InfiniumOmni5-4v1-2_A1-b36-strand.zip
InfiniumOmni5-4v1-2_A1-b37-strand.zip
InfiniumOmni5-4v1-2_A1-b38-strand.zip

HumanOmni5Exome-4v1_A
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-b36-strand.zip
HumanOmni5Exome-4v1-1_A-b37-strand.zip
HumanOmni5Exome-4v1-1_A-b38-strand.zip
Source Strand
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-b36-strand.zip
HumanOmni5Exome-4v1-2_A-b37-strand.zip
HumanOmni5Exome-4v1-2_A-b38-strand.zip

InfiniumOmni5Exome-4v1-3_A1
InfiniumOmni5Exome-4v1-3_A1-b36-strand.zip
InfiniumOmni5Exome-4v1-3_A1-b37-strand.zip
InfiniumOmni5Exome-4v1-3_A1-b38-strand.zip

HumanCytoSNP-12v1-0_D
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-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-b36-strand.zip
humancytosnp-12v2_h-b37-strand.zip
humancytosnp-12v2_h-b38-strand.zip

HumanCytoSNP-12v2-1_H
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-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-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-b36.source.zip
humancytosnp-12v2-1_l-b37.source.zip
humancytosnp-12v2-1_l-b38.source.zip

cytosnp-850k_b
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-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-b36-strand.zip
humancore-12v1-0_a-b37-strand.zip
Updated Versions with INDEL alleles corrected
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-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-b36-strand.zip
humancore-24-v1-0-manifest-file-a-b37-strand.zip
humancore-24-v1-0-manifest-file-a-b38-strand.zip

InfiniumCore-24v1-1_A1
InfiniumCore-24v1-1_A1-b36-strand.zip
InfiniumCore-24v1-1_A1-b37-strand.zip
InfiniumCore-24v1-1_A1-b38-strand.zip

Immuno_BeadChip_11419691_B
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-b36-strand.zip
InfiniumImmunoArray-24v2-0_A-b37-strand.zip
InfiniumImmunoArray-24v2-0_A-b38-strand.zip

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

HumanExome-12v1_A
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-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-b36-strand.zip
HumanExome-12v1-2_A-b37-strand.zip
HumanExome-12v1-2_A-b38-strand.zip

InfiniumExome-24v1-1_A1
InfiniumExome-24v1-1_A1-b38-strand.zip
InfiniumExome-24v1-1_A1-b37-strand.zip
InfiniumExome-24v1-1_A1-b36-strand.zip

HumanCoreExome-12v1-0_B
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-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-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-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-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-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-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-b36-strand.zip
InfiniumCoreExome-24v1-1_A-b37-strand.zip
InfiniumCoreExome-24v1-1_A-b38-strand.zip

InfiniumCoreExome-24v1-2_A
InfiniumCoreExome-24v1-2_A1-b36-strand.zip
InfiniumCoreExome-24v1-2_A1-b37-strand.zip
InfiniumCoreExome-24v1-2_A1-b38-strand.zip

InfiniumCoreExome-24v1-3_A1
InfiniumCoreExome-24v1-3_A1-b36-strand.zip
InfiniumCoreExome-24v1-3_A1-b37-strand.zip
InfiniumCoreExome-24v1-3_A1-b38-strand.zip

Cardio-Metabo_Chip_11395247_A
Cardio-Metabo_Chip_11395247_A-b36-strand.zip
Cardio-Metabo_Chip_11395247_A-b37-strand.zip
Cardio-Metabo_Chip_11395247_A-b38-strand.zip

Original Cardio-Metabo_Chip_11395247_A files, for reference only
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-b36-strand.zip
cardio-metabo_chip_11395247_c-b37-strand.zip
cardio-metabo_chip_11395247_c-b38-strand.zip

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

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

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

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

InfiniumPsychArray-24v1-2_A1
InfiniumPsychArray-24v1-2_A1-b36-strand.zip
InfiniumPsychArray-24v1-2_A1-b37-strand.zip
InfiniumPsychArray-24v1-2_A1-b38-strand.zip

InfiniumPsychArray-24v1-2_A2
InfiniumPsychArray-24v1-2_A2-b36-strand.zip
InfiniumPsychArray-24v1-2_A2-b37-strand.zip
InfiniumPsychArray-24v1-2_A2-b38-strand.zip

PsychChip_15048346_B
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-b36-strand.zip
PsychChip_v1-1_15073391_A1-b37-strand.zip
PsychChip_v1-1_15073391_A1-b38-strand.zip

GSAMD-24v1-0_20011747_A1
GSAMD-24v1-0_20011747_A1-b36-strand.zip
GSAMD-24v1-0_20011747_A1-b37-strand.zip
GSAMD-24v1-0_20011747_A1-b38-strand.zip

GSAMD-24v2-0_20024620_A1
GSAMD-24v2-0_20024620_A1-b36-strand.zip
GSAMD-24v2-0_20024620_A1-b37-strand.zip
GSAMD-24v2-0_20024620_A1-b38-strand.zip

GSA-24v1-0_A1
GSA-24v1-0_A1-b36-strand.zip
GSA-24v1-0_A1-b37-strand.zip
GSA-24v1-0_A1-b38-strand.zip

GSA-24v1-0_A2
GSA-24v1-0_A2-b36-strand.zip
GSA-24v1-0_A2-b37-strand.zip
GSA-24v1-0_A2-b38-strand.zip

GSA-24v1-0_A6
GSA-24v1-0_A6-b36-strand.zip
GSA-24v1-0_A6-b37-strand.zip
GSA-24v1-0_A6-b38-strand.zip

GSA-24v2-0_A1
GSA-24v2-0_A1-b36-strand.zip
GSA-24v2-0_A1-b37-strand.zip
GSA-24v2-0_A1-b38-strand.zip

GSCA-24v1-0_20010441_A1
GSCA-24v1-0_20010441_A1-b36-strand.zip
GSCA-24v1-0_20010441_A1-b37-strand.zip
GSCA-24v1-0_20010441_A1-b38-strand.zip

GSCA-24v2-0_20023496_A1
GSCA-24v2-0_20023496_A1-b36-strand.zip
GSCA-24v2-0_20023496_A1-b37-strand.zip
GSCA-24v2-0_20023496_A1-b38-strand.zip

OncoArray-500K-B
OncoArray-500K_B-b36-strand.zip
OncoArray-500K_B-b37-strand.zip
OncoArray-500K_B-b38-strand.zip

OncoArray-500K-C
OncoArray-500K-C-b36-strand.zip
OncoArray-500K-C-b37-strand.zip
OncoArray-500K-C-b38-strand.zip

Consortium-OncoArray_15047405_A
Consortium-OncoArray_15047405_A-b36-strand.zip
Consortium-OncoArray_15047405_A-b37-strand.zip
Consortium-OncoArray_15047405_A-b38-strand.zip

NeuroX_15036164_A
NeuroX_15036164_A-b36-strand.zip
NeuroX_15036164_A-b37-strand.zip
NeuroX_15036164_A-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

Mapping250K_Nsp.na32.annot-b37-strand.zip
Mapping250K_Sty.na32.annot-b37-strand.zip

Mapping250K_Nsp.na32.annot-b38-strand.zip
Mapping250K_Sty.na32.annot-b38-strand.zip

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

GenomeWideSNP_6.na33.annot-b37-strand.zip
GenomeWideSNP_6.na33.annot-b38-strand.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