Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
CNVnator Install Instructions dmacmillan Bioinformatics 25 09-26-2016 02:59 AM
couldn't run CNVnator menenuh Bioinformatics 39 07-29-2014 12:48 PM
CNVnator for Non-human data BertieWooster Bioinformatics 0 06-07-2011 11:34 AM
SAM result format required in cufflinks arthur.yxt Bioinformatics 15 11-12-2010 02:11 AM
Convert MAQ,SOAP alignment result to ACE format baohua100 Bioinformatics 0 03-02-2009 02:01 AM

Thread Tools
Old 06-30-2011, 09:08 PM   #1
Junior Member
Location: China

Join Date: May 2011
Posts: 6
Default CNVnator: The format of cnv result

I know CNVnator has been used in 1000 Genomes Project. But there is little of material to explain the format of CNV result. Is there anyone know the format of cnv result? For example:
deletion chr10:6070441-6074520 4080 0.674906 0.00834134 72162.3
It is very easy to understand the first three column mean, but is there any can explain the rest of column mean?
zhk is offline   Reply With Quote
Old 07-01-2011, 11:50 AM   #2
Junior Member
Location: boston

Join Date: Mar 2011
Posts: 3

This is what I got from the author of CNVnator:

CNV_type coordinates CNV_size normalized_RD p-val1 p-val2

normalized_RD -- normalized to 1.
p-val1 -- is calculated using t-test statistics.
p-val2 -- is from probability of RD values within the region to be in
the tails of gaussian distribution describing frequencies of RD values in bins.
bioworker is offline   Reply With Quote
Old 07-06-2011, 06:42 PM   #3
Junior Member
Location: China

Join Date: May 2011
Posts: 6

Thx bioworker,
I think it will help me a lot.
zhk is offline   Reply With Quote
Old 08-02-2011, 01:38 PM   #4
Compendia Bio
Location: Ann Arbor

Join Date: Oct 2010
Posts: 35

Do the graphs make any sense? It would be great if any of you can explain it to me.

I graphed the below region and here is what I get:
duplication chr1:172376901-172381900	5000	10.2	2.54996e-10	2.65008e-29
DineshCyanam is offline   Reply With Quote
Old 08-19-2011, 05:57 PM   #5
Location: United States, TN

Join Date: Jul 2010
Posts: 15

So is there any rules should be used to filter the results based on p-val1 or p-val2? Or all the output on screen are candicate?
Hit is offline   Reply With Quote
Old 10-26-2011, 05:20 PM   #6
Location: Seattle

Join Date: Mar 2009
Posts: 18

same question: how to filter result, and which p-val should be considered?
Mark.hz is offline   Reply With Quote
Old 07-31-2014, 10:52 AM   #7
Location: US

Join Date: Apr 2010
Posts: 63

same doubt - how to filter the CNVs.
Maybe p-value of <0.01 or <0.05
And about the size of CNVs?
clarissaboschi 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 06:57 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO