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bcftools
is used in a specific use case ingenotype_snps
:This only seems to work with
bcftools>1.11
(looks like older versions can't handle the-r
flag with remote vcf files because they insist on the index first).This check should invoke
bcftools
with something similar to this use case.The
bioconda
recipe forHATCHet
should be modified to needbcftools>=1.11