VQSRTranche FILTER error

[huangk-000]

Hi,

I caught the below error as I ran the command :
${vcfanno} -base-path ${gemini_data} -lua custom.lua test.conf demo.vcf.gz | bgzip > demo.anno.vcf.gz

The files that I used are attached (Archive.zip). Could you please help take a look? Thanks!

============================================= vcfanno version 0.3.2 [built with go1.12.1]

see: https://github.com/brentp/vcfanno

vcfanno.go:115: found 17 sources from 8 files api.go:796: FILTER error: ##FILTER=. [line: 4] FILTER error: ##FILTER=. [line: 5] FILTER error: ##FILTER=. [line: 6] FILTER error: ##FILTER=. [line: 7]

If you have encountered an error, please include:

• [x] minimal conf and lua files that you are using.
• [x] urls or actual files for annotations in conf file.
• [x] minimal query file.
• [x] the command you used to invoke vcfanno
• [x] the full error message

[brentp]

hmm. my vcf parser is expecting a Description= field for FILTER headers. I'll see if I can relax this for next version, meanwhile, you can get around this by adding ,Description="something" before the > in your vcf header.

[brentp]

by my reading of the spec, the FILTER header should have description, so this is a bug in whatever is generating your VCF, not in vcfanno or vcfgo.

[huangk-000]

Thanks a lot! The issue is gone after I added the description.

[huangk-000]

Thanks a lot! The issue is gone after I added the description.