Annotated txt and csv files show empty columns in SIFT,Polyphen2, Mutation tester and other columns
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12 months ago

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

annotation annovar • 484 views
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  1. Don’t use ALL CAPS. It’s rude.
  2. Use the 101010 option to format your code. The quote button adds block-quote formatting, not code formatting.
  3. Do not use sudo to run simple programs.
  4. Open CSV files in plain text editors not Excel.
  5. Follow this guide to add images: How to add images to a Biostars post
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