SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Question on calling SNPs using samtools/bcftools nkwuji Bioinformatics 6 02-19-2013 09:52 AM
calling SNPs in haploid genomes d17 Genomic Resequencing 27 10-01-2012 07:06 AM
GATK UnifiedGenotyper calling way too many SNPs in vcf swbarnes2 Bioinformatics 0 08-17-2011 02:33 PM
calling Heterozygous SNPs with samtools mpileup egatti Bioinformatics 1 07-21-2011 09:16 AM
calling SNPs asankaf General 2 02-04-2009 07:45 PM

Reply
 
Thread Tools
Old 02-21-2011, 03:21 AM   #1
Kasycas
Member
 
Location: Dublin, Ireland

Join Date: Sep 2009
Posts: 22
Default calling SNPs for prokaryotes

Hi,

I have genomic prokaryotic data and I want to look at SNPs between my data and the existing published data for very similar species. However, where MAQ worked well previously with Illumina data, I now have 454 reads and the BWA/samtools workflow with the pileup command seems to give information on different alleles where heterozygosity exists.

Has anyone worked with 454 data from a prokaryote to call SNPs and how so?

Thanks for the help!
Kasycas is offline   Reply With Quote
Old 02-21-2011, 03:54 AM   #2
nickloman
Senior Member
 
Location: Birmingham, UK

Join Date: Jul 2009
Posts: 356
Default

I tend to use the gsMapper component of Newbler (supplied by Roche with the 454 instrument) for SNP calling.
nickloman is offline   Reply With Quote
Old 02-21-2011, 04:11 AM   #3
Kasycas
Member
 
Location: Dublin, Ireland

Join Date: Sep 2009
Posts: 22
Default

Thanks Nickloman. I hadn't used this part of Newbler before. I'll check it out.
Kasycas is offline   Reply With Quote
Old 02-28-2012, 02:33 AM   #4
Kasycas
Member
 
Location: Dublin, Ireland

Join Date: Sep 2009
Posts: 22
Default

Back on this topic, is GATK ok to use for the detection of prokaryotic SNPs with Illumina data? A lot of the information I'm reading refers to human data so I'm just worried I'd use it incorrectly.

The -D parameter worries me too as you need to specify a .rod file of which there seems only to be human versions...
Kasycas 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 01:58 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO