api.go:789: unexpected header line

[BriMeireles]

Hello,
I tried to run vcfanno with my files (grch37.vcfanno.conf and out-ensemble.vcf.gz) and also tried to run your example (tests/testVA/). Both times, I found the same error:

• Command that I used:
  vcfanno grch37.vcfanno.conf out-ensemble.vcf.gz

• Error:

vcfanno version 0.3.1 [built with go1.11]

see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:115: found 48 sources from 8 files
api.go:789: unexpected header line:

I checked the vcf files and both have a header and the other tools recognized the format as vcf without any problem.
I search online but I don't find any information regarding this error. Can you give me some suggestion to solve this problem?

Thank you,
Best regards,

[syouligan]

Hi @BriMeireles Did you figure out what was going on with this? I am encountering the same error. Thanks!

[brentp]

can you narrow it down to 1 file and then paste the header of that vcf in this issue? then I can fix or help.

[syouligan]

Hi Brent,
Thanks for the epic tool and getting involved.
I have found a solution to this problem in that a data file was called a .vcf when in actual fact it was a .tsv (it only has 5 columns, #chr, pos, ref, alt, value).
When I ran vcfanno on this file without a header it returned three values for each variant, one for each possible ref/alt combination indicating it wasnt recognising the specific ref/alt combination.
When I ran it with a header designating ref/alt yet retaining the .vcf file type it produced the unexpected header error as sited above.
When I changed to a .tsv with the header all was resolved so I assume the .vcf dictates vcfanno file processing?
Sorry for the hassle and thanks for the help.
Cheers

[brentp]

yes. that sounds right. it uses the file extension to "sniff" the file type. it mostly works, but has problems like you encountered here.