SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SNP function prediction in non-human species spark Bioinformatics 7 01-22-2013 01:45 AM
Anyone knows know to access the Human Epigenome Project database.. mandova General 0 12-20-2011 05:49 AM
ChIP-Seq: hmChIP: a database and web server for exploring publicly available human an Newsbot! Literature Watch 1 12-04-2011 02:33 AM
what next after recalibration? adrian Bioinformatics 0 12-14-2010 05:08 PM
SNP Database with Solexa/Illumina Reads foolishbrat Illumina/Solexa 0 10-05-2009 01:54 AM

Reply
 
Thread Tools
Old 05-23-2012, 12:05 PM   #1
Xin Fan
Junior Member
 
Location: US

Join Date: May 2012
Posts: 3
Default How to do the recalibration of non-human species without good SNP database

Hi all,

I am dealing with the genome data of one bird, there are only a few studies about this bird (thus I do not have good SNP data to do the recalibration). I wonder how can I do the recalibration.

I found a suggestion from GATK website:
http://www.broadinstitute.org/gsa/wik...

They said we can bootstrap a database of known SNPs. However, I still have some questions.

1. When I do the initial round of SNP calling on my unrecalibrated data, Should I use any conditions or not? My colleagues are genotyping other genomes. When they do the recalibration (also without good SNP database), they are only requiring that genotypes containing an SNV had a genotype quality score ≥10. If I need to do the same thing as they did, what threshold should I use? They have high coverage genome (>20X), whereas my bird genome is low coverage (15X, after running DepthOfCoverage).

2. They also said "These steps could be repeated several times until convergence". Could anyone please provide some further information about this?

Thanks,
Xin Fan is offline   Reply With Quote
Old 05-24-2012, 09:40 AM   #2
Xin Fan
Junior Member
 
Location: US

Join Date: May 2012
Posts: 3
Default

Any ideas?
Xin Fan is offline   Reply With Quote
Old 05-24-2012, 05:46 PM   #3
aaronh
Member
 
Location: California

Join Date: Sep 2008
Posts: 45
Default

Things that people have been doing include:
taking the intersection of multiple snp callers
using the hard filters
using the top x percent

By convergence, they mean use one of the above sets as truth, rerun the calibration on all of them, use one of the above methods agains, rerun the calibration and so on until your set of snps stops changing.
aaronh is offline   Reply With Quote
Old 05-24-2012, 06:01 PM   #4
Xin Fan
Junior Member
 
Location: US

Join Date: May 2012
Posts: 3
Default

Thanks, it seems that I have to run it several times and try different thresholds.
Xin Fan is offline   Reply With Quote
Reply

Tags
gatk, non-human, recalibration

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 11:27 AM.


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