Strand Data

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
This automates all the three steps detailed on this link: HumanHap550-2v3_B

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

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.

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

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