Assign RSID to ID . / blank column in vcf file
I have vcf file which ID column has input: "." output: chr1:82154 or rs4477212. I am doing using bcftools with the command:
bcftools annotate -a All_SNP.vcf.gz -c ID -o File.vcf.gz input.vcf.gz
Because All_SNP.vcf.gz has chr information as numeric while input.vcf has chr1.
I tried with snpsift tool which is not doing in correct manner, generated file lost some columns.
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