Closed liserjrqlxue closed 3 years ago
if you decompose both the query and annotation vcf, then concat should be fine as it still matches on REF, ALT and POS. Is there a reason that won't work for you?
Thanks for your suggest. But the query vcf is directly created from GATK and multi allelic variants indcate genotype is '1/2', so I think modify annotation vcf may be more suitable for me.
if you decompose that GATK vcf with bcftools norm or vt decompose+normalize, then the 1/2 will be turned into two variants, each with genotype ./1 and ./1. most software will then be able to handle that correctly.
I'm testing result of
vcfanno
for databases like hgmd pro which vcf may not be prefect. I found that one variant may have multi record like:If I use
self
in case that input vcf may have multi alleles in one poistion,vcfanno
only annotate the last record.If I use
concat
,vcfanno
can annotate all record, but not suitable for multi alleles in one poistion.Is there a simple way to solve this issue, or should I modify the hgmd vcf?
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