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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.
<div class="mw-collapsible" style="width:500px">''Command to use at SeqShop Workshop:''<div class="mw-collapsible-content"> ${GC}/bin/vt profile_indels -g ${SS}/ref22/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"</div></div>
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If you are running ''Commands outside the workshop, you will need to update indel.reference.txt to point to the reference files.of SeqShop Workshop:''
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Outside the workshop, you need to update indel.reference.txt to point to the reference files.
cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt
*'''Replace the path to the reference files with the path to your seqshop example directory.'''
*:[[File:IndelRef.png]]
 
${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"
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${GC}/bin/vt profile_indels -g ${SS}/ref22/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"
* When running outside the workshop, use ${OUT}/indel.reference.txt instead of ${SS}/ref22/indel.reference.txt
data set
Sensitivity 69.6% <br>
dbsnp #Indels from dbSNP
A-B 405 404 [0.68] A&B 208 209 [0.79] B-A 494 493 [2.0304] Precision 3334.91% Sensitivity 29.68%
Ins/Del ratios: Reference alignment based methods tend to be biased towards the detection of deletions. This provides a useful measure for discovery Indel sets to show the varying degree of biasness. It also appears that as coverage increases, the ins/del ratio tends to 1.
We perform the same analysis for the failed variants again, the relatively low overlap with known data sets imply a reasonable tradeoff in sensitivity and specificity.
<div class="mw-collapsible" style="width:500px">''Command to use at SeqShop Workshop:''<div class="mw-collapsible-content"> ${GC}/bin/vt profile_indels -g ${SS}/ref22/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "~PASS"</div></div><div class="mw-collapsible mw-collapsed" style="width:500px">''Command outside of SeqShop Workshop:''<div class="mw-collapsible-content"> ${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "~PASS"</div></div> 
data set

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