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brentp / vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5
MIT License
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does this warning mater?| WARNING: using op 'self' when with Number='1' can result in out-of-order values when the query is multi-allelic #128

Closed liserjrqlxue closed 4 years ago

liserjrqlxue commented 4 years ago

I annote ExAC 'AN_Adj' with op 'self' and got out-of-order warning:

api.go:811: WARNING: using op 'self' when with Number='1' for 'AN_Adj' from 'ExAC.r0.3.1.sites.vep.vcf.gz' can result in out-of-order values when the query is multi-allelic
api.go:812:        : this is not an issue if the query has been decomposed.

Does this mater for multi-allelic query now?

I checked Annotate Clinvar With ExAC. It also use 'self' for ’AN_Adj'.

brentp commented 4 years ago

it's just a warning. If your vcf has REF=A and ALT=C,G and the clinvar vcf has a variant for A/C and A/G then your field with Number=1 will actually have 2 values. In the annotate clinvar with ExAC example, both VCFs have been decomposed and normalized. That is the best way to be sure your annotations are consistent.

liserjrqlxue commented 4 years ago

Query vcf decomposed is not simple work for me. I used postannotation to add AF_Adj and AF_EAS to ExAC itself and got a new file as annotate db. I think this can solve this issue and annote fast.