I am trying to retrieve a .fasta file from a large .vcf file
in order to run bcftools' consensus tool i need to bgzip compress the .vcf file and then index it with tabix, nevertheless, when attempting to compress the file largefile.vcf, i get the next error:
"[bgzip] Value too large for defined data type: largefile.vcf"
i tried to compress it using gzip, and it compressed it successfuly, anyways, when i tried to index the resulting largefile.vcf.gz from the gzip compression, i got an error because it is a GZIP file, and not a BGZIP file which is the one needed.
anyone knows why bgzip tool finds the value to large, and not the gzip tool?, i need to get the file bgzip compressed in order to follow my workflow.
Any help would be greately apreciated.