Open BriMeireles opened 5 years ago
Hi @BriMeireles Did you figure out what was going on with this? I am encountering the same error. Thanks!
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.
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
yes. that sounds right. it uses the file extension to "sniff" the file type. it mostly works, but has problems like you encountered here.
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:
see: https://github.com/brentp/vcfanno
vcfanno.go:115: found 48 sources from 8 files api.go:789: unexpected header line: