How is vcf-merge handling different INFO for a single variant?
I imputed several different datasets with the Michigan imputation server and downloaded the output dose.vcf.gz files. I then merged them together by chromosome. I have used both vcf-merge and bcftools merge. My question is, for the same variant, r-square imputation quality can be different between datasets; how is these merging commands dealing with that? I think this is important for downstream analysis. Thanks in advance!
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Please read the bcftools manual:
Thank you! Exactly what I was looking for. I just want to confirm vcf-merge is following the same default, getting INFO from the first input file. I couldn't find it in the vcftools documentation.
AFAIK vcftools is obsolete, there's no feature that bcftools or other tools such as vt/GATK SelectVariants don't cover.