ok, so here we go:
I used the link of free DNA file converter:
https://tendna.com/en/dna-converter
The option of raw data was from AncestryDNA to 23andMe format:
Then I strip my AncestryDNA header up to rsid chromosome position allele1 allele 2:
And now it looked like this:
(I sent it to my virtual machine because I have there Admixtools, Plink and Eigentools).
I convert my 23andmelike file to Plink using this command:
plink --23file 23andmelike.txt Smith John --out mydata
(My name is not Smith John, I just write as an example).
Then I run it:
So I got 4 files: mydata.bed, mydata.bim, mydata.fam and mydata.log
I opened the mydata.fam and I changed manually the -9 to 1:
Smith John 0 0 1 -9 ->
Smith John 0 0 1 1
Then I converted Plink format files to PACKEDANCESTRYMAP format, but first I used to have familynames: NO in the par.PACKEDPED.PACKEDANCESTRYMAP file but I changed to
familynames: YES
It looks like this:
genotypename: mydata.bed
snpname: mydata.bim
indivname: mydata.fam
outputformat: PACKEDANCESTRYMAP
genotypeoutname: mydata.geno
snpoutname: mydata.snp
indivoutname: mydata.ind
familynames: YES
I run it with the command:
convertf -p par.PACKEDPED.PACKEDANCESTRYMAP
I received 3 new files: mydata.geno, mydata.ind and mydata.snp
Now I tried to merged them with the AADR files (Both are in the PACKEDANCESTRYMAP format), but adding 3 parameters in the merge_param.par file, besides the geno1, snp1 and ind1 were mydata files and geno2, snp2 and ind2 were the AADR ones.
Like this:
geno1: mydata.geno
snp1: mydata.snp
ind1: mydata.ind
geno2: v62.0_1240k_public.geno
snp2: v62.0_1240k_public.snp
ind2: v62.0_1240k_public.ind
genooutfilename: mydata_merged_with_1240k.geno
snpoutfilename: mydata_merged_with_1240k.snp
indoutfilename: mydata_merged_with_1240k.ind
outputformat: PACKEDANCESTRYMAP
docheck: YES
strandcheck: YES
So I run this command:
mergeit -p merge_param.par
So something went wrong again, but now the "allele funny" did not appear, so this time what did it happen?
