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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. |
− | | + | <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"> | | <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.
| + | ''Commands outside of SeqShop Workshop:'' |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
| + | 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 | | cp ${SS}/ref22/indel.reference.txt ${OUT}/indel.reference.txt |
| | | |
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| *'''Replace the path to the reference files with the 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]] |
| + | |
| + | ${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> |
| </div> | | </div> |
| | | |
− | ${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 | | data set |
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| Sensitivity 69.6% <br> | | Sensitivity 69.6% <br> |
| dbsnp #Indels from dbSNP | | dbsnp #Indels from dbSNP |
− | A-B 405 [0.68] | + | A-B 404 [0.68] |
− | A&B 208 [0.79] | + | A&B 209 [0.79] |
− | B-A 494 [2.03] | + | B-A 493 [2.04] |
− | Precision 33.9% | + | Precision 34.1% |
− | Sensitivity 29.6% | + | Sensitivity 29.8% |
| | | |
| 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. | | 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. |
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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. |
| | | |
− | ${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" | + | <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 | | data set |