Hi all,
I am trying to annotate my imputed genetic file using bcftools and then want to convert it to plink.
bcftools index -t ro_imputed_hrcgrch37.R2_0.3.vcf.gz
bcftools annotate \
-a $DATADIR/ro_imputed_hrcgrch37.R2_0.3.vcf.gz \
-c ID $REF/All_20180423.vcf.gz \
--output-type z \
-o $DATADIR/ro_imputed_hrcgrch37.R2_0.3.vcf_dbSNP151.vcf.gz
This seems to work but my samples are removed. Consequently, when I try to convert to binary plink files, it doesn't work because it says I have no samples. Can anyone give advice on what I've done wrong?
Many thanks
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