VEP [E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip

Question

[Filago]

Hello!

I installed VEP with the INSTALL.pl script without any error, but when running it

the following error occurs:

[E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip
./annotate_vep.sh: line 16: 14589 Segmentation fault      

Here you can find my command:

/home/user/ensembl-vep/vep --offline --cache -i /home/user/Desktop/vep_test/all_merged.vcf.gz --buffer_size 5000 --no_stats --biotype --sift p --polyphen p --assembly GRCh37 --force_overwrite --tab --output_file /home/user/Desktop/vep_test/test_vep.txt

Any idea how to solve this issue?

Best,

Andreas

Answer 1

[zx8754]

Error is clear, the file is not bgzipped, gunzip your file, then use bgzip to zip with index, see http://www.htslib.org/doc/bgzip.html

[Filago]

Hello. I tried this:

bgzip --index merged.vcf

and here is the resulting file-type:

merged.vcf.gz: Blocked GNU Zip Format (BGZF; gzip compatible), block length 4599

However, still the same error occurs.

[Filago]

Furthermore, I tried the command with just merged.vcf and not merged.vcf.gz (should work with VEP), but still the same error occurs. Thus it seems to me like the error does not target my input VCF file...but what else?

[zx8754]

Check chrom names, they must match with reference, chr1 vs 1.

[Filago]

In the fasta file and my VCF its "1" and not "chr1"

[Filago]

Ok, I think I found the source of the error. The fasta file downloaded by the install script is gziped but not bgziped...why? I will try bgzip it and see what happens...

[Filago]

That solved it!