Annotation header Ex. SnpEffVersion

[raonyguimaraes]

Hi Brent,

I am wondering how I could keep certain vcf header values after using vcfanno for example:

##SnpEffVersion and ##SnpEffCmd

After using vcfanno to merge this vcf with a VEP(ed) vcf I don't see these fields anymore.

Is there a way to include these headers in the output?

Here is my config.toml

[[annotation]]
file="/home/raony/dev/pynnotator/pynnotator/tests/ann_sample.100.hg38/snpeff/snpeff.output.vcf.gz"
fields = ["ANN"]
names = ["snpeff_eff"]
ops=["first"]

[[annotation]]
file="/home/raony/dev/pynnotator/pynnotator/tests/ann_sample.100.hg38/vep/vep.output.sorted.vcf.gz"
fields = ["CSQ"]
names = ["vep_csq"]
ops=["first"]

[brentp]

I see the utility in this. I might accept a PR for this. But you can see how it could get unwieldy to handle everything. If you just allow headers like this, it could be something like:

[[annotation]]
file="/home/raony/dev/pynnotator/pynnotator/tests/ann_sample.100.hg38/vep/vep.output.sorted.vcf.gz"
fields = ["CSQ"]
names = ["vep_csq"]
ops=["first"]
headers=["SnpEffVersion", "SnpEffCmd"]

[C-Gouveia]

Hi Brent,

Regarding this, is there anyway of adding a new line to the header of the annotated file where the vcfanno version is specified?

Thank you

[brentp]

@C-Gouveia this is now implemented and in release v0.3.3

[C-Gouveia]

Awesome! Thank you

[raonyguimaraes]

thank you!