Changes

== Goals of This Session ==

== Goals of This Session ==

* What we want to learn is calling large deletions using GenomeSTRiP implemented in [[GotCloud]] pipeline

* What we want to learn is calling large deletions using GenomeSTRiP implemented in [[GotCloud]] pipeline

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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, June 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.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, June 2014#GotCloud_BAM_Index_File|GotCloud BAM Index File]]

* BAMs->SVs rather than BAMs->SNPs

* BAMs->SVs 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, June 2014#Examining_GotCloud_SnpCall_Input_files|GotCloud SnpCall Input Files]]

If you want to check if you still have the bam index file, run

If you want to check if you still have the bam index file, run

We will use the same configuration file we used for the GotCloud Align tutorial.

We will use the same configuration file we used for the GotCloud Align tutorial.

See [[SeqShop:_Sequence_Mapping_and_Assembly_Practical#GotCloud Configuration File|SeqShop: Alignment: GotCloud Configuration File]] for more details

See [[SeqShop:_Sequence_Mapping_and_Assembly_Practica, June 2014l#GotCloud Configuration File|SeqShop: Alignment: GotCloud Configuration File]] for more details

* Note we want to limit snpcall to just chr22 so the configuration already has <code>CHRS = 22</code> (default was 1-22 & X).

* Note we want to limit snpcall to just chr22 so the configuration already has <code>CHRS = 22</code> (default was 1-22 & X).

In principle, the metadata can be created from the input BAM files by running the following command

In principle, the metadata can be created from the input BAM files by running the following command

  #time perl ${SS}/svtoolkit/bin/genomestrip.pl -run-metadata --conf ${SS}/gotcloud.conf --numjobs 2 --base-prefix ${SS} --outdir ${OUT}

  perl ${SS}/svtoolkit/bin/genomestrip.pl -run-metadata --conf ${SS}/gotcloud.conf --numjobs 2 --base-prefix ${SS} --outdir ${OUT}

'''WAIT!!!!! DO NOT RUN THIS COMMAND, because it will take ~50 minutes to finish'''.

'''WAIT!!!!! DO NOT RUN THIS COMMAND, because it will take ~50 minutes to finish'''.