Allele coding BIM and Genotypes in SNPmatrix (0,1,2,3). Coding doubt.
Hi, I have the following situation for a SNP:
In the BIM file Contig position A1 A2 3551 58921 C T
Reference is T
In the SNPmatrix it gets coded as 3 when T/T and 1 when C/C, 2 T/C.
Given the reference is T and for individuals that are T/T shouldn't it be coded 1?
Many thanks
• 2,339 views
•
link
written
by
j.j.stocks •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Convert alleles from Illumina 1/2 format to ACGT format?
written by dam4l
-
How to get RSIDs of indels from GWAS summary statistics
written by Fede_Santos95 •
-
R reshape data
written by Cindy •
-
Rounding error in allele frequency estimates in PLINK
written by GabrielMontenegro
-
A2 different between PLINK .bim file and .frq file?
written by curious
-
calculate fst for every allele in any position
written by mostafarafiepour
-
Calculating Heterozygosity for each SNPs.
written by mostafarafiepour
-
When to supsect flips after merging two datasets by plink?
written by khn
-
Reshape tabular data frame to wide format
written by friasoler •
-
Convert Sequence Alignment Into A Prettybase Polymorphic Sites Table And Calculate Pi, Theta, And T…
written by anin.gregory
