VCF files that are filtered using bcftools and have their data compressed by specifying -O z as part of the command can't be imported into R because of the error "scanBcfHeader(bf) : [internal] _hts_rewind() failed". Decompressing the file and re-compressing it using the R function bgzip enables it to be successfully imported, but it seems an inefficient workaround and it's unclear why it's required. This issue has been reported for an older version of VariantAnnotation #22
VCF files that are filtered using bcftools and have their data compressed by specifying
-O zas part of the command can't be imported into R because of the error "scanBcfHeader(bf) : [internal] _hts_rewind() failed". Decompressing the file and re-compressing it using the R functionbgzipenables it to be successfully imported, but it seems an inefficient workaround and it's unclear why it's required. This issue has been reported for an older version of VariantAnnotation #22