255
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchCreated page with 'Introduction to New Students * R/C++/perl/python code snipplets / toy examples of various packages [[https://statgen.sph.umich.edu/wiki/Category:Code_Samples Internal Resources…'
Introduction to New Students
* R/C++/perl/python code snipplets / toy examples of various packages
[[https://statgen.sph.umich.edu/wiki/Category:Code_Samples Internal Resources]]
* How to use git
Git is a version control software. We have useful library codes and useful applications (see Sequence Analysis Tools section in [[http://genome.sph.umich.edu/wiki/Main_Page]]).
A dedicated introduction page is here:
[[https://statgen.sph.umich.edu/wiki/How_To_Use_Git How to use git]]
* Tools howto - with examples - samtools, PLINK, MERLIN, bwa, etc
Samtools [[http://samtools.sourceforge.net/samtools.shtml Manual]]
PLINK [[http://pngu.mgh.harvard.edu/~purcell/plink/ Homepage]]
MERLIN [[http://www.sph.umich.edu/csg/abecasis/merlin/ Homepage]]
BWA[[http://bio-bwa.sourceforge.net/bwa.shtml Homepage ]]
* SAM/VCF format documentation
[[http://samtools.sourceforge.net/SAM1.pdf SAM specification]]
[[http://genome.sph.umich.edu/wiki/VCF VCF specification]]
* UNIX 101
CSG Documentation [[http://csg.sph.umich.edu/docs/ AWK, BASH, UNIX commands and etc.]]
* Collection of useful resources/links
Group Chat [[https://statgen.sph.umich.edu/wiki/Instant_Messaging instant Messaging]]
* R/C++/perl/python code snipplets / toy examples of various packages
[[https://statgen.sph.umich.edu/wiki/Category:Code_Samples Internal Resources]]
* How to use git
Git is a version control software. We have useful library codes and useful applications (see Sequence Analysis Tools section in [[http://genome.sph.umich.edu/wiki/Main_Page]]).
A dedicated introduction page is here:
[[https://statgen.sph.umich.edu/wiki/How_To_Use_Git How to use git]]
* Tools howto - with examples - samtools, PLINK, MERLIN, bwa, etc
Samtools [[http://samtools.sourceforge.net/samtools.shtml Manual]]
PLINK [[http://pngu.mgh.harvard.edu/~purcell/plink/ Homepage]]
MERLIN [[http://www.sph.umich.edu/csg/abecasis/merlin/ Homepage]]
BWA[[http://bio-bwa.sourceforge.net/bwa.shtml Homepage ]]
* SAM/VCF format documentation
[[http://samtools.sourceforge.net/SAM1.pdf SAM specification]]
[[http://genome.sph.umich.edu/wiki/VCF VCF specification]]
* UNIX 101
CSG Documentation [[http://csg.sph.umich.edu/docs/ AWK, BASH, UNIX commands and etc.]]
* Collection of useful resources/links
Group Chat [[https://statgen.sph.umich.edu/wiki/Instant_Messaging instant Messaging]]
