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Old 01-12-2009, 10:00 AM   #1
doxologist
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Question SNP detection

Any suggest good SNP detection software for short-reads. Currently, the software I find are mostly alignment of individual tags. Any experience with software that consolidates the tags and calls SNPs?

Does the Illumina BeadStudio or NextGenE do any of this?
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Old 01-12-2009, 10:04 AM   #2
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Maq will align to your reference, and output all the differences it finds into a nice SNPs file.
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Old 01-12-2009, 10:16 AM   #3
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Can you first align with Bowtie? Then use MAQ for this?
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Old 01-12-2009, 10:42 AM   #4
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Maq does alignments itself. If Maq can be tricked into using Bowtie output, I don't know how to do it.
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Old 01-12-2009, 11:17 AM   #5
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thanks. since bowtie is so much faster than MAQ... perhaps to harness both would be an option. Hmm... more digging needed. :P
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Old 01-13-2009, 09:16 AM   #6
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PLoS ONE. 2008;3(12):e4012. Epub 2008 Dec 24.
Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing.
Shen Y, Sarin S, Liu Y, Hobert O, Pe'er I.

Although this paper compared SOLiD and solexa platforms for variation detection, it also compared MAQ and corona_lite. MAQ mapped more reads to the refereces, but corona-lie pick up the false negative by MAQ using the same filering rules. This was caused by the way MAQ streats two-color encoding.
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Old 01-13-2009, 09:25 AM   #7
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thanks. I was aware of this paper.. but didn't know they included MAQ as well.
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Old 05-17-2009, 05:41 AM   #8
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Quote:
Originally Posted by doxologist View Post
Any suggest good SNP detection software for short-reads. Currently, the software I find are mostly alignment of individual tags. Any experience with software that consolidates the tags and calls SNPs?

Does the Illumina BeadStudio or NextGenE do any of this?

Maybe this one could help you: MapView 3.3 - a short reads alignment viewer with genetic variation analysis It has "SNP detection".
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Old 05-18-2009, 08:11 AM   #9
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Quote:
Originally Posted by doxologist View Post
Any suggest good SNP detection software for short-reads. Currently, the software I find are mostly alignment of individual tags. Any experience with software that consolidates the tags and calls SNPs?

Does the Illumina BeadStudio or NextGenE do any of this?
NextGENe does that .. consolidate or condense reads to make up longer fragments to be then used for alignment to reference .. a neat approach to reduce error rates I would say..
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Old 05-26-2009, 01:47 AM   #10
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MAQ's paper can be found in Genome reserach Genome Res. 2008 18: 1851-1858 originally published online August 19, 2008, doi:10.1101/gr.078212.108:
Mapping short DNA sequencing reads and calling variants using mapping quality scores

BTW, SOAP SNP detection had come out, you can try.
Genome Res. published online May 6, 2009, doi:10.1101/gr.088013.108:
SNP detection for massively parallel whole-genome resequencing
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Old 06-23-2009, 02:48 PM   #11
roedel
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Default Bowtie Maq

Heng Li & Richard Durbin recently published a new mapping package that uses Burrows-Wheeler transformation, this might combine the fast mapping of Bowtie with the maq SNP-calling

Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform

http://bioinformatics.oxfordjournals...bstract/btp324

Quote:
Originally Posted by doxologist View Post
thanks. since bowtie is so much faster than MAQ... perhaps to harness both would be an option. Hmm... more digging needed. :P
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Old 11-12-2009, 01:14 PM   #12
EdK
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Talking about SNP detection, does anybody know if it is possible to use a whole genome or a single chromosome as reference in CLC bio for SNP detection? I tried but it doesnt recognize the file as a reference and it works only with genebank files that have annotation and so on... how can I do that?
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Old 07-11-2010, 09:08 PM   #13
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Was looking for SNP detection software as well and ran into this post.

I've used SOAPsnp but just tried Mapview 3.3 and am very happy with it. It allows one to call SNPs based on adjustable quality score, coverage value and variant frequency. For a GUI it is very fast too!
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Old 07-12-2010, 04:41 AM   #14
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MagicViewer will meet your need,you can try it.
MagicViewer is a sophisticated assembly visualization and genetic variation annotation tool for next-generation sequencing data.
http://bioinformatics.zj.cn/magicviewer/

Last edited by baby1885; 07-12-2010 at 04:43 AM.
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Old 09-06-2010, 07:49 AM   #15
mayar
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You can first align with bowtie (using the -S option to get a SAM output) and then use SAMtools pileup and varFilter to get Consensus or SNP calling.

http://samtools.sourceforge.net/cns0.shtml

Hope this is handy.
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