SIFT command line help (non-human)

Question

[bruce.moran]

Hi all,

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  ...

Command:

java -jar ~/SIFT/SIFT4G_Annotator_v1_0.jar -c -t -i ~/input.vcf -d ~/SIFT/UMD3.1.74/ -r ~/SIFT/

Help much appreciated.

[Giovanni M Dall'Olio]

it will be easier to help you if you include an example of input files, and the full command line you executed.

[bruce.moran]

Edited, how do you tag code in Biostars?

[Giovanni M Dall'Olio]

Just select the text, and then in the "Text" menu choose the Code style.