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# Look at the filtered file.
# Look at the filtered file.
#: <pre>zless -S output/vcfs/chr22/chr22.filtered.vcf.gz</pre>
#: <pre>zless -S output/vcfs/chr22/chr22.filtered.vcf.gz</pre>
#: Scroll down some: [[File::screenshot]]
#: Scroll down some: [[File::SnpVcfOutput.png|700px]]
## Check for the expected SNP at 22:36661906
## Check that GotCloud found the expected SNP at 22:36661906
##:<pre>tabix output/vcfs/chr22/chr22.filtered.vcf.gz 22:36661906 |head -1</pre>
##:<pre>tabix output/vcfs/chr22/chr22.filtered.vcf.gz 22:36661906 |head -1</pre>
#:[[File::screenshot]]
#:[[File::SnpTabix.png|700px]]
# Look at the summary information
# Look at the summary information
#:<pre>cat output/vcfs/chr22/chr22.filtered.sites.vcf.summary</pre>
#:<pre>cat output/vcfs/chr22/chr22.filtered.sites.vcf.summary</pre>
#:[[File::screenshot]]
#:[[File:SnpSummary.png|700px]]
#:*'''To understand how to interpret the filtering summary statistics, please refer to [[Understanding vcf-summary output]]'''
=== Run GotCloud Indel ===
=== Run GotCloud Indel ===
