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Tutorials

665 bytes added, 15:17, 16 November 2019
<pre>
docker pull statisticalgenetics/annovar
statgen-setup login --tutorial annovar
</pre>
==Gemini==
* [https://drive.googlegithub.com/filestatgenetics/dstatgen-courses/0B2pJ9cgevF3sTS1DeGxYalFTN00blob/view Bam files for master/handout/Gemini.docx Gemini exercise<nowiki>[DOCX]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial gemini</pre> The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
==GenABEL==
To run the exercise from docker image provided,
<pre>docker pull statisticalgenetics/igv
statgen-setup login --tutorial igv
</pre>
==Linkage/FastLinkage==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/blob/master/SEQLinkagehandout/linkage_intro_ex_berlin_2018_with_pg_numMLINK.pdf Linkage Introduction LINKAGE Exercise <nowiki>[PDFDOCX]</nowiki>]  To run the exercise from docker image provided, <pre>statgen-setup login --tutorial mlink</pre> The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
<!--
To run the exercise from docker image provided,
<pre>docker pull statisticalgenetics/popgen
statgen-setup login --tutorial popgen
</pre>
To run the exercise from docker image provided,
<pre>docker pull statisticalgenetics/pseq
statgen-setup login --tutorial pseq
</pre>
To run the exercise from docker image provided,
<pre>docker pull statisticalgenetics/regression
statgen-setup login --tutorial regression
</pre>
==SLINK==
* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/filesblob/tutorialsmaster/seqsparkhandout/slink_ex_shortSlink.pdf doc SLINK Exercise <nowiki>[PDFDOCX]</nowiki>]
To run the exercise from docker image provided,
To install from packages, follow the configuration steps above <pre>statgen-setup login --tutorial slink</pre> The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and run can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the following command-tutorials these instructions].
<pre>sudo apt-get install slink-tutorial</pre>
The exercise's files will then be installed in the folder ''/home/shared/slink''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
==SUPERLINK==
To run the exercise from docker image provided,
<pre>docker pull statisticalgenetics/vat
statgen-setup login --tutorial vat
</pre>