SnpEFF generates value as true instead of 1

Question

[win]

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.

[Devon Ryan]

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.