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

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jasdeep kaur

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Jul 8, 2021, 12:03:24 PM7/8/21
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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
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