Vcfanno bgzf error

Question

[bioinformatics98]

Hello all,

Whenever I run vcfanno on my samples, I get this error:

vcfanno.go:115: found 12 sources from 3 files
vcfanno.go:156: falling back to non-bgzip
api.go:796: bix: error opening bgzf reader for example/exac.vcf.gz: bgzf: could not determine block size

Can somebody please explain what this error means and why this is happening? How can I solve this error?

Thank you!

[Pierre Lindenbaum]

how was compressed example/exac.vcf.gz ? gzip ? this is wrong. The file must be compressed with bgzip of bcftools.

the output of file example/exac.vcf.gz should be gzip compressed data, **extra field**

[bioinformatics98]

I am not sure how it was compressed as I got it from here: https://github.com/brentp/vcfanno When I tried running this example/exac.vcf.gz on Brentp's example input file called query.vcf.gz --> my code worked perfectly! I did exactly how it says to do under the "Example" section of Brentp's github page and it worked perfectly on their example files --> it is just not working on my files.

[Pierre Lindenbaum]

$ wget -q -O - "https://github.com/brentp/vcfanno/blob/master/example/exac.vcf.gz?raw=true" | file -
/dev/stdin: gzip compressed data, extra field

the file is ok