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  • ANNOVAR reporting the depth score

    Hello.

    I am using ANNOVAR and have successfully created the .avinput files for my vcf files correctly. If I examine the .avinput, the first 5 entries of each line correctly display the hetereozygosity, quality, and depth score.

    however when I call table_annovar.pl, the depth score and zygosity is not reported onto the columns.


    I am interested mainly in having the depth score tabulated... advice on how to attain these scores?

    Should I use the VariantTools package for reporting the dp score?

    Thank you so much in advance

  • #2
    is your data like this format:
    1,14398,14400,TGT,-,"ncRNA_exonic","DDX11L1,WASH7P",NA,NA,NA,"Score=0.993729;Name=chr9:10843",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA

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    • #3
      DP score in ANNOVAR

      thank you for the response

      the solution for reporting DP score in the annovar_table is using the parameter -otherinfo.

      the website shows that otherinfo is used for region analysis of variants, but it also includes the DP score.

      Thank you

      AC

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