Difference between revisions of "How-to/SNP detection"

Latest revision as of 13:53, 13 November 2012

Note: This content has been ported to the new WikiBook project: http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS)/DNA_Variants

@@ Line 1: / Line 1: @@
-== SNP detection using next gen data ==
+<big>
+<big>
+'''Note''': This content has been ported to the new WikiBook project:
+http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS)/DNA_Variants
-[[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
+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
-[[Freebayes]]
+</big>
+</big>
-[[SNVMix]]
-[[SOAPsnp]]
-[[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
-[[GATK]]