Problem of .dose.vcf.gz files as input for bcftools for annotation purposes

[rskl92]

Hi,

I am trying to use bcftools to annotate the chromosome:position with rsids. Normally, this code should work with .vcf.gz files but it doesn't and reports the following error " Failed to open -: not compressed with bgzip". Has this been encountered previously with Michigan imputed files? I would appreciate your advice!

bcftools annotate
--output-type v
--remove ID
--set-id +'%CHROM:%POS:%REF:%ALT'
chr21.dose.vcf.gz
| bcftools annotate
--annotations All_20170710.vcf.gz
--columns ID
--output-type v
| plink
--vcf /dev/stdin
--keep-allele-order
--double-id
--make-bed --out chr21

Thanks