Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Phil Colson reporting in! Philcolson Introductions 1 07-06-2012 05:28 PM
454 quality score, z-score,.. nii 454 Pyrosequencing 2 10-14-2011 10:46 AM
What's maximum depth and minimum depth? slny Bioinformatics 0 03-17-2011 11:13 AM
ELAND reporting more than 2 mismatches? kch Illumina/Solexa 3 11-30-2009 08:45 AM
Fastq quliaty score and MAQ output quality score baohua100 Bioinformatics 1 02-19-2009 10:21 AM

Thread Tools
Old 06-10-2014, 12:06 PM   #1
Senior Member
Location: Los Angeles

Join Date: Nov 2013
Posts: 142
Default ANNOVAR reporting the depth score


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, 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
arcolombo698 is offline   Reply With Quote
Old 06-19-2014, 12:18 AM   #2
Junior Member
Location: hK

Join Date: Jun 2014
Posts: 5

is your data like this format:
yuelincoln is offline   Reply With Quote
Old 06-19-2014, 11:09 AM   #3
Senior Member
Location: Los Angeles

Join Date: Nov 2013
Posts: 142
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

arcolombo698 is offline   Reply With Quote


Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:45 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO