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| − | = SNP detection =
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| − | = Decision Helper =
| + | '''Note''': This content has been ported to the new WikiBook project: |
| − | I want to quickly call SNP versus a reference
| + | http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS)/DNA_Variants |
| − | =>Freebayes, samtools
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| | + | Previous contributors should ensure they take proper credit for their work here: |
| | + | http://en.wikibooks.org/w/index.php?title=Next_Generation_Sequencing_(NGS)/Authors |
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| − | = Software Packages =
| + | </big> |
| − | | + | </big> |
| − | == Free Software ==
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| − | === Freebayes ===
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| − | [[Freebayes]] is the scuccessor of Poly- Giga- and BAMBayes and should be much faster than these. Like these it relies on BAM files. It has also been described in some more detail by its developed on [http://biostar.stackexchange.com/questions/613/what-methods-do-you-use-for-in-del-snp-calling Biostar]
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| − | * Pros
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| − | ** very easy to run for simple SNP calling
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| − | === GATK ===
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| − | The Genome Analysis toolkit [[GATK]] allows multiple steps. The authors used their pipeline for variant calling using the NA12878 exome data set and compared their results to those of Crossbow (which uses SOAPsnp). Based on these results they concluded that crossbow had a lower spcecificity.
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| − | One easy way to to run GATK and other tools might be to use this [https://github.com/vlandham/variant_pipeline variant pipeline] mentioned on [http://biostar.stackexchange.com/questions/8260/workflow-or-tutorial-for-snp-calling Biostar]
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| − | * Pro
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| − | ** Likely relatively specific
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| − | * Con
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| − | ** relatively complex pipelines
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| − | === MAQ ===
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| − | [[MAQ]]
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| − | === samtools ===
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| − | [[samtools]] using the pilepup or mpileup pipeline
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| − | http://samtools.sourceforge.net/mpileup.shtml
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| − | 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.
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| − | http://seqanswers.com/forums/showthread.php?t=11965
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| − | === ssahaSNP ===
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| − | [[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 ===
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| − | [[SOAPsnp]]
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| − | === SNVMix ===
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| − | [[SNVMix]]
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| − | == Further Reading Material and References ==
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