Vcfanno bgzf error
0
0
Entering edit mode
18 months ago

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!

vcfanno • 361 views
ADD COMMENT
0
Entering edit mode

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**

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode
$ 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

ADD REPLY

Login before adding your answer.

Traffic: 1067 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6