Lecture4_my-script-with-perl_mark-for-snp

Jimmy（jmzeng1314@outlook.com）

Keywords: snp/ transitions/ transversions/

The standard set of categories we have used for many sequencing projects is as follows:

· 1. CpG transitions

· 2. CpG transversions

· 3. C:G transitions

· 4. C:G transversions

· 5. A:T transitions

· 6. A:T transversions

The result will just like below :

GGC>TGC 0 G T 2

GGC>CGC 0 G C 2

GGC>GAC 1 G A 1

GGC>GTC 1 G T 2

GGC>GCC 1 G C 2

GGC>GGA 2 C A 2

GGC>GGT 2 C T 1

GGC>GGG 2 C G 2

GGG>AGG 0 G A 3

GGG>TGG 0 G T 4

GGG>CGG 0 G C 4

GGG>GAG 1 G A 3

GGG>GTG 1 G T 4

GGG>GCG 1 G C 4

GGG>GGA 2 G A 3

GGG>GGT 2 G T 4

GGG>GGC 2 G C 4

useful links :

http://www.broadinstitute.org/cancer/cga/mutsig_run

http://www.bio-info-trainee.com/?p=1176

https://www.mun.ca/biology/scarr/Transitions_vs_Transversions.html

https://en.wikipedia.org/wiki/Transversion

http://www.uvm.edu/~cgep/Education/Mutations.html