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901 bytes removed
, 14:03, 19 May 2015
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| 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. |
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− | ''Command to use at SeqShop Workshop:''
| + | Currently indel.reference.txt needs absolute paths to the reference files, so update indel.reference.txt to point to the reference files. |
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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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− | </div>
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− | </div>
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− | ''Commands outside of SeqShop Workshop:''
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− | Outside the workshop, you need to update indel.reference.txt to point to the reference files.
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| cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt | | cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt |
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| ${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" | | ${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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− | </div>
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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. | | 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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− | <div class="mw-collapsible mw-collapsed" style="width:500px">
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− | ''Command to use at SeqShop Workshop:''
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− | <div class="mw-collapsible-content">
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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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− | </div>
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− | </div>
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− | <div class="mw-collapsible" style="width:500px">
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− | ''Command outside of SeqShop Workshop:''
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− | <div class="mw-collapsible-content">
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| ${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" | | ${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>
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− | </div>
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