Difference between revisions of "How-to/SNP detection"
< How-to
(→SNP detection using next gen data) |
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| − | + | = SNP detection = | |
| + | = Decision Helper = | ||
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| + | = Software Packages = | ||
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| + | == Free Software == | ||
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| + | === Freebayes === | ||
[[Freebayes]] | [[Freebayes]] | ||
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| − | [[ | + | === GATK === |
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| + | [[GATK]] | ||
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| + | === MAQ === | ||
| + | [[MAQ]] | ||
| + | === samtools === | ||
[[samtools]] using the pilepup or mpileup pipeline | [[samtools]] using the pilepup or mpileup pipeline | ||
http://samtools.sourceforge.net/mpileup.shtml | http://samtools.sourceforge.net/mpileup.shtml | ||
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| − | [[ | + | === ssahaSNP === |
| + | [[ssahaSNP]] - ssahaSNP is a polymorphism detection tool. It detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. More tuned for ABI Sanger reads. Developers are Adam Spargo and Zemin Ning from the Sanger Centre. Compaq Alpha, Linux-64, Linux-32, Solaris and Mac | ||
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| + | === SOAPsnp === | ||
| + | [[SOAPsnp]] | ||
| − | [[ | + | === SVNMix === |
| + | [[SNVMix]] | ||
Revision as of 16:54, 12 August 2011
Contents
SNP detection
Decision Helper
Software Packages
Free Software
Freebayes
GATK
MAQ
samtools
samtools using the pilepup or mpileup pipeline http://samtools.sourceforge.net/mpileup.shtml
This thread here describes some potential problems that occur when using the BAQ parameter. (In effect it recommends to turn it off, if one uses e.g. BWA that finds indels. http://seqanswers.com/forums/showthread.php?t=11965
ssahaSNP
ssahaSNP - ssahaSNP is a polymorphism detection tool. It detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. More tuned for ABI Sanger reads. Developers are Adam Spargo and Zemin Ning from the Sanger Centre. Compaq Alpha, Linux-64, Linux-32, Solaris and Mac
