indexVcf Fails if VCF File Not Compressed

Bioconductor / VariantAnnotation

Annotation of Genetic Variants

https://bioconductor.org/packages/VariantAnnotation

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indexVcf Fails if VCF File Not Compressed #33

Closed DarioS closed 5 years ago

DarioS commented 5 years ago

I looked at the documentation of indexVcf and it says nothing about requiring compressed files. However,

indexVcf("primaryTissue.merged.annotated.vcf")
Error in value[[3L]](cond) : file does not appear to be bgzip'd

mtmorgan commented 5 years ago

this is a limitation of the documentation; the constraint comes from underlying htslib / bcftools. Compressed files can be created with Rsamtools::bgzip().