Changes

== Setup in person at the SeqShop Workshop ==

== Setup in person at the SeqShop Workshop ==

''This section is specifically for the SeqShop Workshop computers.''

''This section is specifically for the SeqShop Workshop computers.''

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''If you are not running during the SeqShop Workshop, please skip this section.''

''If you are not running during the SeqShop Workshop, please skip this section.''

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== Setup when running on your own outside of the SeqShop Workshop ==

== Setup when running on your own outside of the SeqShop Workshop ==

''This section is specifically for running on your own outside of the SeqShop Workshop.''

''This section is specifically for running on your own outside of the SeqShop Workshop.''

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''If you are running during the SeqShop Workshop, please skip this section.''

''If you are running during the SeqShop Workshop, please skip this section.''

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This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]]

This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical, December 2014|Alignment Tutorial]]

It also uses the bam.index file created in the SnpCall Tutorial.  If you have not yet run that tutorial, please follow the directions at: [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical#GotCloud_BAM_Index_File|GotCloud BAM Index File]]

It also uses the bam.list file created in the SnpCall Tutorial.  If you have not yet run that tutorial, please follow the directions at: [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical, December 2014#GotCloud_BAM_List_File|GotCloud BAM List File]]

* BAMs->INDELs rather than BAMs->SNPs

* BAMs->INDELs rather than BAMs->SNPs

If you want a reminder, of what they look like, here is a link to the previous tutorial : [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical#Examining_GotCloud_SnpCall_Input_files|GotCloud SnpCall Input Files]]

If you want a reminder, of what they look like, here is a link to the previous tutorial : [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical, December 2014#Examining_GotCloud_SnpCall_Input_files|GotCloud SnpCall Input Files]]

== Running GotCloud Indel ==

== Running GotCloud Indel ==