Problems with Reference alleles at VCF files
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18 months ago

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 vcf reference • 313 views
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Did you try anything like simple text manipulation with awk?

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