3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSeqShop: Variant Calling and Filtering for INDELs Practical, December 2014 (view source)
Revision as of 15:11, 6 December 2014
, 15:11, 6 December 2014→Comparison with other data sets
It is usually useful to examine the call sets against known data sets for the passed variants.
It is usually useful to examine the call sets against known data sets for the passed variants.
<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
cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt
Edit indel.reference.txt and specify the correct path to ${SS}
Edit indel.reference.txt and specify the correct path to ${SS}
nedit ${OUT}/indel.reference.txt
nedit ${OUT}/indel.reference.txt
*'''Replace all occurrences of <code>username</code> with your username (or the correct path to your seqshop example directory).'''
*'''Replace the path to the reference files with the path to your seqshop example directory.'''
*:[[File:IndelRef.png]]
*:[[File:IndelRef.png]]
</div>
</div>
${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"
${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"
