I have 2 vcf files for the same positions but with different individuals which I would like to merge.
However, in one of the files some of my variants have a
. in the ALT field, which I would like to replace by the corresponding allele.
I've tried to obtain those alternatives alleles from my other vcf which looks apparently correct.
I'm using the following command of
plink --vcf my.vcf --const-fid 0 --a1-allele ALT.txt 5 3 '#' --recode --out myfile.mod.vcf
ALT.txt contains two columns:
ALTfield of my other vcf file (I've tried both with and without header). Still, the program says:
Error: Fewer tokens than expected on line 1 of --a1-allele file.
I don't know what I'm doing wrong so I would appreciate it if anyone sees something that I'm not seeing or if anyone recommends other tools. Thank you very much in advanced :)