I have checked the raw data and there may be a way to make it compatible with GEDMatch by reformatting it to look like a 23andMe file. What I did is open a text editor and delete all these (use search and replace):
. . VC=SNV GT 0/0
. . VC=SNV GT 0/1
. . VC=SNV GT 1/0
. . VC=SNV GT 1/1
After that, you can remove the spaces between the alleles like that (for each combination)
search for 'G A' replace by 'GA'
This is easy enough. The problem is that 23andMe uses the following order:
rsid chromosome position genotype
While Living DNA uses that order:
chromosome position rsid genotype
So if we could find a way to move the rsid from third to first position that would make the file identical to the 23andMe layout. I will ask them if they can do it. If not, does anybody here have programming skills to create a file converter to move the position of the rsid? The command would be something like "cut rs* + tab" then "paste at the beginning of same line". It sounds easy enough, but unfortunately I don't have the programming skills to do it.
Dienekes used this script to standardise 23andMe and FTDNA genomes:
Code:
standardize <- function(genotypefile, company='23andMe')
{
if (company=='23andMe') {
X<-read.table(genotypefile)
}
if (company=='ftdna') {
X<-read.table(genotypefile, sep=',',skip=1)
}
write.table(X[order(X[,1]),],file='genotype.txt',quote=F,row.names=F,col.names=F)
}
This only removes the file headers, but it could be a variant of that using the same script in R.
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Originally Posted by ajc347
