vcftools and bcftools disagree
Hello,
I'm trying to impute my data using HRC (sanger server). For that I validated and annotated my vcf using GATK and then prepared my vcf as requested on the site. Then I checked my vcf using vcf-validator which finds no allele error for me but when setting up the file on the site, bcftools tells me that 3/4 of the lines do not have the right reference allele. Why Vcftools and bcftools do not agree and how to fix this problem and thus allow an imputation of my data without removing 3/4 of my lines.
I'm trying to impute my data using HRC (sanger server). For that I validated and annotated my vcf using GATK and then prepared my vcf as requested on the site. Then I checked my vcf using vcf-validator which finds no allele error for me but when setting up the file on the site, bcftools tells me that 3/4 of the lines do not have the right reference allele. Why Vcftools and bcftools do not agree and how to fix this problem and thus allow an imputation of my data without removing 3/4 of my lines.