I tried annotating my vcf file in ANNOVAR using the below mentioned command but I am unable to get the SIFT,Polyphen2 , Mutationtester and other score values in the output txt and csv file. The corresponding columns in csv file show empty values. The size of the txt and csv files is also different i.e csv(140MB) and txt file (427 MB) Also, the text when opened in excel shows -csvout as values in all the respective prediction score columns. I want to attach a screenshot to depict the same also but I am unable to upload here.
PLEASE SOMEONE TELL ME WHY THIS IS HAPPENING??
sudo perl table_annovar.pl multisamples1000gPhase1.vcf.avinput humandb/ -buildver hg19 -out 1000ganno -remove -protocol refGene,cytoBand,1000g2014oct_all,snp138,dbnsfp30a -operation g,r,f,f,f -nastring . -csvout