Question: Problems with Reference alleles at VCF files
0
gravatar for epifaniarango
9 months ago by
epifaniarango0 wrote:

Hi!

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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