Entering edit mode
9.4 years ago
alex
▴
250
Trying to index vcf file but getting the following
tabix -p vcf dbsnp_138.hg19.vcf.gz
Not a BGZF file: dbsnp_138.hg19.vcf.gz
tbx_index_build failed: dbsnp_138.hg19.vcf.gz
Thoughts on how to proceed? Thanks!
@Sean Davis you just saved me a lot of frustration. I found this after a few searches and it worked. THanks
I had the same problem: when I compressed with
gunzip <file>.vcf
tabix gave the error:tbx_index_build failed:<file>.vcf.gz
but it worked with `bgzip <file>.vcf.Of course it does.
bgzip
does blockwise (therefore the b in bgzip) compression of the file, whichtabix
relies on. That enablestabix
to quickly retrieve data by only very partially decompressing a (sometimes hugh) file, guided by the index.gzip
does not do blockwise compression.