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Question: How to Get only one annotation with the SnpEff annotation?
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gravatar for mhmtgenc85
12 months ago by
mhmtgenc85 • 30
Turkey
mhmtgenc85 • 30 wrote:

Dear All,

As you know when annotationg a vcf file each line might have more than one annotation but I would like to get only one annotation for a line? the first one only if possible.

So thanks in advance.
snp snpeff variation annotation • 554 views
ADD COMMENT • link •
modified 12 months ago by Pierre Lindenbaum ♦ 121k • written 12 months ago by mhmtgenc85 • 30
1

a variant can overlap multiple transcripts with different consequences; So why would you want to do this ?

ADD REPLY • link modified 12 months ago • written 12 months ago by Pierre Lindenbaum ♦ 121k

Yeah you are right but for some reason I only would like to get only the first annotation. :)

ADD REPLY • link written 12 months ago by mhmtgenc85 • 30
0
gravatar for Pierre Lindenbaum
12 months ago by
Pierre Lindenbaum ♦ 121k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 121k wrote:

using vcffilterjdk: http://lindenb.github.io/jvarkit/VcfFilterJdk.html

 java -jar dist/vcffilterjdk.jar -e 'final String ann="ANN";List<Object> atts = variant.getAttributeAsList(ann); return atts.size()<=1 ? variant : new VariantContextBuilder(variant).attribute(ann,atts.get(0)).make();' input1.vcf
ADD COMMENT • link written 12 months ago by Pierre Lindenbaum ♦ 121k
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