I am trying to run SIFT4G and finding it giving me no results! I am working on cows, so I D/L the reference from here which is pretty up to date, so I was hopeful. I have GATK-called VCF, so I tried putting that in 'dry'. No joy. I looked at the input format info and so input only first 5 columns of VCF. Same thing happens (excerpt for brevity):
Chromosome WithSIFT4GAnnotations WithoutSIFT4GAnnotations Progress 19 0 0 Completed : 1/31 15 0 0 Completed : 2/31 17 0 0 Completed : 3/31
Anyone had similar issues? I know I ran it correctly as I am doing everything the help page suggest (-c -t, and any combination of them!). I have also annotated with SNPdat which returns plenty of nonsense and some stop mutations so I know there is that info in there.
head -n 1 input.vcf 10 357766 . T C 902.12 PASS INFO GT:AD:DP:GQ:PL ...
java -jar ~/SIFT/SIFT4G_Annotator_v1_0.jar -c -t -i ~/input.vcf -d ~/SIFT/UMD3.1.74/ -r ~/SIFT/
Help much appreciated.