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Comparison with other data sets
It is usually useful to examine the call sets against known data sets for the passed variants.
In order to do this<div class="mw-collapsible mw-collapsed" style="width:500px">If you are running outside the workshop, you will need to update indel.reference.txt to point to the reference files.<div class="mw-collapsible-content">
cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt
Edit indel.reference.txt and specify the correct path to ${SS}
nedit ${OUT}/indel.reference.txt
*'''Replace all occurrences of <code>username</code> the path to the reference files with your username (or the correct path to your seqshop example directory).'''
*:[[File:IndelRef.png]]
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${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"

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