Error in output format: the variantFrequencies field of the samples

[algarsi3]

I annotated the "getting started" with the following command:

dotnet bin/Release/netcoreapp3.1/Nirvana.dll \
     -c Data/Cache/GRCh37/Both \
     --sd Data/SupplementaryAnnotation/GRCh37 \
     -r Data/References/Homo_sapiens.GRCh37.Nirvana.dat \
     -i HiSeq.10000.vcf.gz \
     -o HiSeq.10000

When I tried to parse the variants to json in Python, I found the following variant:

{"chromosome":"chr1","position":309,"refAllele":"C","altAlleles":["T"],"quality":0,"filters":["FDRtranche2.00to10.00+"],"strandBias":-5001,"mappingQuality":2112,"cytogeneticBand":"1p36.33","samples":[{"genotype":"0/1","variantFrequencies":[0,0804],"totalDepth":32,"alleleDepths":[103,9]}],"variants":[{"vid":"1-309-C-T","chromosome":"chr1","begin":309,"end":309,"refAllele":"C","altAllele":"T","variantType":"SNV","hgvsg":"NC_000001.10:g.309C>T","gerpScore":0}]},

Which corresponds to the following variant in the original file:

chr1	309	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=153.70;MQ=21.12;MQ0=35;OQ=53.98;QD=0.46;SB=-50.01	GT:AD:DP:GL:GQ	0/1:103,9:32:-18.33,-9.64,-96.32:86.82

Python throws an error because of the following field: "variantFrequencies":[0,0804]

I assume that the correct value should be 0.0804 with a . rather than a , .

[rajatshuvro]

Thanks for pointing this out. We will work on it.