calling SNPs for prokaryotes

Kasycas · 02-21-2011, 03:21 AM

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!

nickloman · 02-21-2011, 03:54 AM

I tend to use the gsMapper component of Newbler (supplied by Roche with the 454 instrument) for SNP calling.

Kasycas · 02-21-2011, 04:11 AM

Thanks Nickloman. I hadn't used this part of Newbler before. I'll check it out.

Kasycas · 02-28-2012, 02:33 AM

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...

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

02-21-2011, 03:21 AM	#1
Kasycas Member Location: Dublin, Ireland Join Date: Sep 2009 Posts: 22	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!

02-21-2011, 03:54 AM	#2
nickloman Senior Member Location: Birmingham, UK Join Date: Jul 2009 Posts: 356	I tend to use the gsMapper component of Newbler (supplied by Roche with the 454 instrument) for SNP calling.

02-21-2011, 04:11 AM	#3
Kasycas Member Location: Dublin, Ireland Join Date: Sep 2009 Posts: 22	Thanks Nickloman. I hadn't used this part of Newbler before. I'll check it out.

02-28-2012, 02:33 AM	#4
Kasycas Member Location: Dublin, Ireland Join Date: Sep 2009 Posts: 22	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...