(SnpEff) SnpSift annotates only the first .vcf line
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7.8 years ago
damian.loska ▴ 20

Hi, I want to annotate my .vcf file based on ExAC database. I'm ONLY interested in AC_EAS tags from the database

I do: java -jar SnpSift.jar annotate -info AC_EAS ExAC_db.vcf.gz my.vcf.gz > out.vcf

however only the first variant in my.vcf.gz is annotated and the tag AC_EAS=0 is addad. All other positions remain empty, without annotations. These positions should be annotated since they exist both in my.vcf.gz and in ExAC_db.vcf.gz

Did you have similar problem?

Thx

SnpSift SnpEff • 2.3k views
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