Question: ANNOVAR Annotation VCF empty
gravatar for frankie.north
2.1 years ago by
frankie.north10 wrote:

Hi all,

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

Many Thanks.

rna-seq annotation vcf annovar • 774 views
ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson25k • written 2.1 years ago by frankie.north10
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Are you working at This appears to be a cluster error. Please try re-running the job. Should it fail again, please submit a bug report and we can review. Include a link to this Biostars post in the comments and be sure to leave the inputs and error datasets undeleted.

Best, Jen, Galaxy team

ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson25k
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