(SnpEff) SnpSift annotates only the first .vcf line
0
0
Entering edit mode
5.1 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 • 1.7k views
ADD COMMENT

Login before adding your answer.

Traffic: 1448 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6