SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GATK snp calling wanguan2000 Bioinformatics 0 11-24-2011 08:23 PM
SNP base calling shuang Bioinformatics 7 10-24-2011 11:50 AM
Samtools SNP calling vidhya Bioinformatics 3 04-07-2011 06:17 AM
What are the SNP calling programs? foxyg Bioinformatics 2 10-08-2010 05:19 AM
MAQ and SNP calling michy Bioinformatics 3 12-11-2009 08:23 AM

Reply
 
Thread Tools
Old 01-21-2011, 06:36 AM   #1
elondin
Junior Member
 
Location: PA

Join Date: Jan 2011
Posts: 2
Default SNP calling

Hi all,

I have a question regarding determing if an identified SNP would be a heterozygote. When looking at the total number of reads for a specific base, what percentage of those reads need to differ from the reference to be considered a heterozygote. For example, if a base has 50 a coverage of 50 reads, but 25% of them differ from the reference would this be called as a heterozygote? Essentially, at what proportion of calls that differ from the reference is a homozygote vs. heterozygote?

Any thoughts?
thanks
elondin is offline   Reply With Quote
Old 01-24-2011, 12:30 AM   #2
flxlex
Moderator
 
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415
Default

The difference from the reference is in a way irrelevant here, I feel. What matters is the amount of reads that show a difference for the organism you sampled. If around 50% shows one base, and the rest shows the other, then the organism you sequenced is a heterozygote at that position, right? How much deviation you can have from 50/50, I don't know, but there will be some spread...
flxlex is offline   Reply With Quote
Old 01-24-2011, 07:29 AM   #3
husamia
Member
 
Location: cinci

Join Date: Apr 2010
Posts: 66
Default

you stated "When looking at the total number of reads for a specific base, what percentage of those reads need to differ from the reference to be considered a heterozygote." I say "When looking at the total number of reads for a specific base, what percentage of those reads need to differ from the reference to be considered a variant?" I have seen cutoff of 15% and 20%. We're only talking about diploid organisms of course. Its a good question, since you have to take into account only true reads.

Last edited by husamia; 01-24-2011 at 07:33 AM.
husamia is offline   Reply With Quote
Old 01-24-2011, 09:59 AM   #4
krobison
Senior Member
 
Location: Boston area

Join Date: Nov 2007
Posts: 747
Default

A number of the SNP callers have attempted to answer this question (with the additional complication that your bases may not all be called to the same confidence) using Bayesian principles; if you really want to understand it, you should study those papers.
krobison is offline   Reply With Quote
Reply

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 06:03 PM.


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