Open francoiskroll opened 4 years ago
I think that the FILTER only gets added if it is not PASS (or .).
I see. Seems like the field is empty in the gnomAD vcf if not PASS, but from what I can see the filter AC0 is always present if PASS is absent? So that should be okay.
Example
from gnomAD vcf:
chr20 4694192 . A T 182 AC0;AS_VQSR AC=0 ...
vcfanno adds annotation:
chr20 4694192 . A T 31.5 PASS ... ;gnomadv3_FILTER=AC0,AS_VQSR;gnomadv3_AC=0 GT 1/1
If useful for a future reader – I'm also able to pull the lcr (low complexity region) filter; for example:
My conf.toml:
[[annotation]] file="gnomad_chr20_4680000to4705000.vcf.gz" fields = ["FILTER", "lcr", "AC"] ops=["self", "self", "self"] names=["gnomadv3_FILTER", "gnomadv3_lcr", "gnomadv3_AC"]
Annotation looks like (this variant is PASS in both my vcf & on gnomAD):
chr20 4694861 . C A 31.5 PASS ... ;gnomadv3_lcr;gnomadv3_AC=86 GT 1/1
Thanks for your help!
That must be me; but I can't seem to find how to pull some specific fields from a gnomAD vcf.
gnomAD vcf file header:
Example of entry from gnomAD vcf file:
Say I want to extract all of the 8 fields above. I'm starting with rs ID / FILTER / AC as a test.
My conf.toml file is:
And my command:
rs ID and AC works great, but I can't seem to get the FILTER out. I have also tried with
fields = ["PASS"]
.Example of entry of my own vcf:
Can you help?