Question: SnpEFF generates value as true instead of 1
gravatar for win
4.3 years ago by
win810 wrote:

I am using SNPEff to annotate our VCF files and it is working fine. But the issues is that at certain annotations it generates a keys values = true. 

When we try to use other programs over such as Wormtable then it seems that a value 1 was expected in place of true.

Is there any way to instruct SNPEff to generate values 1 or some other way we can convert those true to 1.

Commands used for annotations:

java -jar /home/snpEff/SnpSift.jar annotate -v 00-All.vcf in.vcf.gz | bgzip >ann1.vcf.gz
java -Xmx4g -jar /home/snpEff/snpEff.jar eff -v GRCh38.76 ann1.vcf.gz | bgzip > ann.fin.vcf.gz

Thanks in advance.

vcf • 1.1k views
ADD COMMENTlink modified 4.3 years ago by RamRS21k • written 4.3 years ago by win810

Wow, that seems like an annoying bug. Please report it to the developers!

As a work around, you could just stick sed in between snpEff and bgzip and just have it do the replacement on the stream.

ADD REPLYlink written 4.3 years ago by Devon Ryan90k
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