error in plink file: Non-ACGTN alternate allele at 1:4635556 .. REF_SEQ:'(null)' vs VCF:'-'

[jasdeep kaur]

Hi all,

I am Imputing genotype data from Sanger imputation server and got this error:

The input file sanity check failed, "bcftools norm -ce" exited with the following message:
>         Non-ACGTN alternate allele at 1:4635556 .. REF_SEQ:'(null)' vs VCF:'-'

How to replace '_' with '(null)' in the vcf file ?

any help is appreciated 

Thanks

Jasdeep