I am trying to run ANNOVAR Annotation tool to remove known SNPs from my VCF file, however everytime I run ANNOVAR the table comes back empty? From what I can see there are no errors with my previous VCF file and it is aligned to hg19, therefore I do not know what I am doing wrong?
This is the vcf for the file prior to this step but when viewing it only comes up with chromosome, position and rsnumber.
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1A-S7 chrM 73 . G A 1695.58 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=3.9638;MQ=59.56;MQ0=0;QD=31.99 GT:AD:DP:GQ:PL 1/1:0,53:53:99:1729,141,0
chrM 150 . T C 7042.74 . AC=2;AF=1.00;AN=2;DP=229;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=6.4380;MQ=59.13;MQ0=0;QD=30.75 GT:AD:DP:GQ:PL 1/1:0,229:229:99:7043,602,0
And this is the error message that comes up cannot stat `output.hg19_multianno.vcf': No such file or directory