Question: Problems with Reference alleles at VCF files
gravatar for epifaniarango
11 days 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 • 52 views
ADD COMMENTlink written 11 days ago by epifaniarango0

Did you try anything like simple text manipulation with awk?

ADD REPLYlink modified 11 days ago • written 11 days ago by ATpoint26k
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