VCF index not created with HTSlib doesn't work

molgenis / vip

Variant Interpretation Pipeline

https://molgenis.github.io/vip/

GNU Lesser General Public License v3.0

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VCF index not created with HTSlib doesn't work #436

Closed dennishendriksen closed 1 year ago

dennishendriksen commented 1 year ago

VCF index created via HTSlib (e.g. BCFtools) adds metadata to the index that is used by bcftools index --stats (context here). This information might not be available when the index is created with other tools, e.g. PyVCF.