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==== Examining Indel Output ====
==== Examining Indel Output ====
# Look inside the output directory to see the new indel directories:
#:<pre>ls output</pre>
#:[[File:IndelSnpOutput.png.png|700px]]
#:#<code>aux</code> - intermediate indel files
#:#<code>final</code> - final output of Indel pipeline
#:#<code>indelvcf</code> - intermediate indel files
#:#<code>gotcloud.indel.conf</code> - file containing all of the configuration settings used for this run of GotCloud
#:#<code>gotcloud.indel.Makefile</code> - Makefile containing commands for this run of GotCloud
#:#<code>gotcloud.indel.Makefile.log</code> - log of the GotCloud run
# Important Indel output is in <code>output/final</code>
#:<pre> ls output/final/</pre>
#: [[File:IndelFinal.png|700px]]
# Look at the final Indel VCF file.
#: <pre>zless output/final/all.genotypes.vcf.gz</pre>
#: Scroll down some: [[File::IndelLess.png|700px]]
## Check that GotCloud found the expected Indel at 22:36662041
##:<pre>tabix output/final/all.genotypes.vcf.gz 22:36662041-36662041|less -S</pre>
#:[[File::IndelTabix.png|700px]]
== Exit & Terminate ==
# Exit from your terminal
# Terminate your Amazon Instance
