I am using plink to to export sequence data in vcf format to a raw file but keep getting the following error at a specific line that halts the entire process:
"ALT allele duplicates REF allele on line 166993 of .vcf file"
using the following command
plink --vcf "infile.vcf.gz" --extract exomeids.txt --out "outfile" --recodeA
When I examine this line I see that all subjects appear to be homozygous (listed as either 0/0 or 1/1). I can remove this exact chromosome or position but then get the same error on a different line. Is there a more succinct way to remove this error than listing all the positions that result in this error?
Note that this position is not one that I want to extract for my results but it is still processed in the initial part of the --out command. I have also used similar commands for other vcf files with no errors so I am curious if something is wrong with the coding on this file since I cannot find documentation of these error elsewhere.
Thanks for your help in advance.