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Old 06-27-2016, 07:59 AM   #1
Location: Barcelona

Join Date: Feb 2012
Posts: 49
Default (SnpEff) SnpSift annotates only the first .vcf line

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?

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