Merge branch 'master' of https://github.com/ISUgenomics/bioinformatic…

…s-workbook

Appendix/Unix/UnixCheatSheet.md

@@ -16,8 +16,9 @@ header:
 | <span style="color:Green">_Command_</span>|<span style="color:Green">_Function_</span>|<span style="color:Green">_Syntax/example usage_</span> |
 |`ls` 	|list contents	|`ls` <span style="color:Red">[OPTIONS] DIRECTORY</span>|
 |`pwd`	|print working directory	|`pwd`|
-|`cd`|change directory	|`cd` ~ or `cd` 		#home directory|
-| | 			|`cd` .. #previous (parent directory)|
+|`cd`|change directory	|`cd ~` or `cd` 		#home directory|
+| | 			|`cd ..` #"up" a directory (parent directory)|
+| |       |`cd -` # previous directory |
 
 ## File/Directory operations
 
@@ -206,4 +207,4 @@ header:
 |||`module avail`			# lists available modules|
 |||`module unload` <span style="color:Red">PROGRAM</span>	# unloads module|
 
-PS: An A-Z Index of the Bash command line for Linux can be found at found [Here](http://ss64.com/bash/index.html)
+PS: An A-Z Index of the Bash command line for Linux can be found [here](http://ss64.com/bash/index.html)

Appendix/Unix/unix-basics-1.md

@@ -453,7 +453,7 @@ ls Deleteme3
 
 ### Warning about deleting files and directories
 
-In Unix there is no undo command.  If you delete a file it is gone.  There is no trash bin.  The next two commands are very powerful commands and cna lead to unfortunate losses if not used with care. With that said you can only delete files you have created.  So it is impossible to delete someone else files without permission.
+In Unix there is no undo command.  If you delete a file it is gone.  There is no trash bin.  The next two commands are very powerful commands and can lead to unfortunate losses if not used with care. With that said you can only delete files you have created.  So it is impossible to delete someone else files without permission.
 
 ## `rmdir` -- <span style="color:Blue">R</span>e<span style="color:Blue">m</span>ove <span style="color:Blue">Dir</span>ectory
 This command can remove an empty directory

dataAnalysis/VariantCalling/gatk-dnaseq-best-practices-workflow.md

@@ -12,10 +12,6 @@ header:
 
 # GATK Best Practices Workflow for DNA-Seq
 
-## Introduction
-
-Link Andrew's GATK introduction here or borrow his text.
-
 ## Dataset
 
 For this tutorial we will use the dataset from BioProject [PRJEB18647](https://www.ncbi.nlm.nih.gov/bioproject/PRJEB18647). This dataset has Illumina short reads for four different populations of _Arabidopsis halleri_ subsp. _halleri_ (Aha18, AhaN1, AhaN3, AhaN4) and was originally used for estimating genomic diversity and population differentiation for these 4 populations ([Fischer _et. al_.,](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3459-7)).