I just extracted the report of the Illumina SNP array genotyping using Illumina genome studio. To be specific, I extracted genotypes of the top strand for each locus. Interestingly, none of the loci displayed Thymine (T) as one of the alleles in a genotype. How can it be possible? Is it because the Illumina defined "Bottom" and "Top" in a certain way where "T" always gets the "bottom" strand designation?
•
written
by
nehal1610.ranabhatt •
1 answer
Illumina uses a custom SNP designation.
Check the post:
Illumina'S Genome Studio Final Report: Forward Or Top Allele?
and the corresponding document here:
https://www.illumina.com/documents/products/technotes/technote_topbot.pdf
and the blog post:
http://onetipperday.sterding.com/2015/12/snp-allele-coding-schema.html
Log in to answer this question.
-
How to convert Illumina SNP ids having mappings to multiple RSID in loci to rsid file ?
written by vasank1958 •
-
How to create proper genotype text file format for use in Coancestry from a vcf file
written by Karen •
-
Reference genome, VCF files, genotype
written by tea.vuki •
-
Illumina Omni2.5 genotyping get actual genotypes.
written by nhaus •
-
Strain Assignments to QTL Data
written by annacsalvador •
-
how to convert top/bot, or plus/minus strand to positive/negative strand
written by lilingjoyo •
-
Concordance NGS and array genotypes
written by genomixer •
-
Convert Plink Ped Format Into Hapmap Format?
written by 2184687-1231-83-
-
How To Retrieve "True" Alleles Of Genotypes From Geo Obtained With Illumina Human610-Quad V1.0?
written by tflutre
-
Top/Bottom Confusion For Illumina Snp Calls
written by Perry •
