How-to/SNP detection
SNP detection using next gen data
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
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
