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Old 06-10-2014, 12:06 PM   #1
arcolombo698
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Location: Los Angeles

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Default 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
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Old 06-19-2014, 12:18 AM   #2
yuelincoln
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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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Old 06-19-2014, 11:09 AM   #3
arcolombo698
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Default 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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