How to detect homozygous SNPs with GigaBayes

fikys · 09-02-2009, 11:00 PM

I have hard time finding SNPs that are homozygous in all 454 reads when compared to the reference sequence (the reference sequence will have the second allele) from MosaikAligner assembly using GigaBayes software. It always reports only those SNPs that are represented by different alleles in the reads:

AAGTTT - reference (1)

AAGTTT
AAGTTT
AACTTT
AACTTT
(G/C) will be reported

AAGTTT - reference (2)

AACTTT
AACTTT
AACTTT
AACTTT

(G/C) will not be reported

I'm using --anchor option to use the reference to call a SNP but it seems still ignoring second type of SNPs.

Can anybody help?

Saffron · 12-10-2009, 09:34 PM

Hi,

I am having the same issue - did you figure out a solution to this?

Thanks.

Saffron

fikys · 12-11-2009, 07:00 PM

Yes, in my case it seem to be conflicting with the fact that I asked for 2X coverage of each allele... could not imagine that this will be applied to the reference sequence allele. These options produced homozygous SNPs together with low-quality heterozygous ones. Had to do a lot of additional filtering of GigaBayes output. I had two individuals that I compared to the same reference sequence.

Command line that generated this output: gigaBayes --gig ./pyrobase/assembly_sen/chr1.gig --sample multiple --sampleDel F --ploidy diploid --anchor --O 4 --CRL 3 --CRU 31 --gff ./pyrobase/chr1.gff

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
mpileup and homozygous snps	grievous	Bioinformatics	5	02-19-2014 05:58 PM
homozygous and heterozygos	asankaf	General	15	04-04-2013 03:03 PM
Homozygous mammal sequence data	dansullivanblk	Bioinformatics	2	02-02-2012 04:36 AM
gigabayes no output	shaohua.fan	Bioinformatics	7	10-16-2010 10:59 AM
RNA-seq to detect expressed SNPs	Melanie	Sample Prep / Library Generation	2	05-13-2010 10:54 AM

09-02-2009, 11:00 PM	#1
fikys Junior Member Location: USA Join Date: Sep 2009 Posts: 2	How to detect homozygous SNPs with GigaBayes I have hard time finding SNPs that are homozygous in all 454 reads when compared to the reference sequence (the reference sequence will have the second allele) from MosaikAligner assembly using GigaBayes software. It always reports only those SNPs that are represented by different alleles in the reads: AAGTTT - reference (1) AAGTTT AAGTTT AACTTT AACTTT (G/C) will be reported AAGTTT - reference (2) AACTTT AACTTT AACTTT AACTTT (G/C) will not be reported I'm using --anchor option to use the reference to call a SNP but it seems still ignoring second type of SNPs. Can anybody help?

12-10-2009, 09:34 PM	#2
Saffron Junior Member Location: Adelaide / London Join Date: Nov 2009 Posts: 2	Hi, I am having the same issue - did you figure out a solution to this? Thanks. Saffron

12-11-2009, 07:00 PM	#3
fikys Junior Member Location: USA Join Date: Sep 2009 Posts: 2	Yes, in my case it seem to be conflicting with the fact that I asked for 2X coverage of each allele... could not imagine that this will be applied to the reference sequence allele. These options produced homozygous SNPs together with low-quality heterozygous ones. Had to do a lot of additional filtering of GigaBayes output. I had two individuals that I compared to the same reference sequence. Command line that generated this output: gigaBayes --gig ./pyrobase/assembly_sen/chr1.gig --sample multiple --sampleDel F --ploidy diploid --anchor --O 4 --CRL 3 --CRU 31 --gff ./pyrobase/chr1.gff