I downloaded 13G VCF files for a set of chimpanzees, from here:
I am trying to index this vcf with
bcftools index -f Pan_troglodytes.vcf.gz
But i get the error:
[E::bgzf_read_block] Invalid BGZF header at offset 12889964510 index: failed to create index for "Pan_troglodytes.vcf.gz"
If I try without the -f flag (bcftools index Pan_troglodytes.vcf.gz) then the error i get is:
index: the input is probably truncated, use -f to index anyway. I deleted the file and re downloaded, but same problem.
The other vcf files I download from this site, eg https://eichlerlab.gs.washington.edu/greatape/data/VCFs/SNPs/Gorilla.vcf.gz work absolutely fine.
Does anyone know what is causing this error, and how to solve it?
Versions: bcftools 1.14-48-g58f886f Using htslib 1.14-22-g3f7e13e