Question: Problems with Reference alleles at VCF files
gravatar for epifaniarango
9 months ago by
epifaniarango0 wrote:


I am having big issues with my vcf files. Some of the SNPs are no variable but instead of having 'N' as value for missing data, my files have a '.' which doesn't allow me to run Beagle. Do you know an easy way to change the missing reference allele to 'N'? Thank you so much for your help


snp reference vcf • 182 views
ADD COMMENTlink written 9 months ago by epifaniarango0

Did you try anything like simple text manipulation with awk?

ADD REPLYlink modified 9 months ago • written 9 months ago by ATpoint36k
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