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#:[[File:SnpSummary.png|700px]]
#:[[File:SnpSummary.png|700px]]
#:*'''To understand how to interpret the filtering summary statistics, please refer to [[Understanding vcf-summary output]]'''
#:*'''To understand how to interpret the filtering summary statistics, please refer to [[Understanding vcf-summary output]]'''
=== Run GotCloud ldrefine ===
Now run GotCloud ldrefine
# <pre>gotcloud ldrefine --conf example/test.conf --outdir output --numjobs 8</pre>
#* The ubuntu user is setup to have the gotcloud program and tools in its path, so you can just type the program name and it will be found
#: [[File:RunIndel.png|700px]]
#:* This will take a few minutes to run.
#:* GotCloud first generates a makefile, and then runs the makefile
# When complete, GotCloud ldrefine will indicate success/failure
#:[[File:LdrefineSuccess.png|700px]]
==== Examining ldrefine Output ====
=== Run GotCloud Indel ===
Now run GotCloud indel
# <pre>gotcloud indel --conf example/test.conf --outdir output --numjobs 8</pre>
#* The ubuntu user is setup to have the gotcloud program and tools in its path, so you can just type the program name and it will be found
#: [[File:RunIndel.png|700px]]
#:* This will take a few minutes to run.
#:* GotCloud first generates a makefile, and then runs the makefile
# When complete, GotCloud indel will indicate success/failure
#:[[File:IndelSuccess.png|700px]]
==== Examining Indel Output ====
