Strand Home

All new new files and tools will from now on be posted to:

strand.org.uk

Please check there for the latest updates and information

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

william

rayner

helmholtz-munich

will

rayner

strand

org

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.

Genotyping chips strand and build files

Please note I have now left the Wellcome Centre for Human Genetics and this page will no longer be updated

All new new files and tools will from now on be posted to:

strand.org.uk

Please check there for the latest updates and information

Illumina data files

Other Allele Sets

Updating the strand and position

Allele Updates

Ref/Alt

Strand and Position Files

Affymetrix data files

Strand and position derived from the Affymetrix releases

Genotyping chips strand and build files

Please note I have now left the Wellcome Centre for Human Genetics and this page will no longer be updated

All new new files and tools will from now on be posted to: strand.org.uk Please check there for the latest updates and information

Illumina data files

Other Allele Sets

Updating the strand and position

Allele Updates

Ref/Alt

Strand and Position Files

Affymetrix data files

Strand and position derived from the Affymetrix releases

All new new files and tools will from now on be posted to:

strand.org.uk

Please check there for the latest updates and information