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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 mw-collapsed" style="width:500px">''Command to use at SeqShop Workshop:''<div class="mw-collapsible-content"> ${GC}/bin/vt profile_indels -g ${SS}/ref22/Currently 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" style="width:500px">''Commands outside of SeqShop Workshop:''<div class="mw-collapsible-content">Outside needs absolute paths to the workshopreference files, you need to so update indel.reference.txt to point to the reference files.
cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt
${GC}/bin/vt profile_indels -g ${OUT}/indel.reference.txt -r ${SS}/ref22/human.g1k.v37.chr22.fa ${OUT}/indel/final/all.genotypes.vcf.gz -i 22:36000000-37000000 -f "PASS"
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We perform the same analysis for the failed variants again, the relatively low overlap with known data sets imply a reasonable tradeoff in sensitivity and specificity.
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''Command to use at SeqShop Workshop:''
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${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"
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''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"
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