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, 15:52, 16 June 2014
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| == Comparison with other data sets == | | == Comparison with other data sets == |
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− | It is usually useful to examine the call sets against known data sets. | + | It is usually useful to examine the call sets against known data sets for the passed variants. |
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| vt profile_indels -g /net/fantasia/home/atks/ref/vt/grch37/indel.reference.txt -r /net/fantasia/home/atks/ref/vt/grch37/hs37d5.fa run/final/all.genotypes.bcf -i 22:36000000-37000000 -f "PASS" | | vt profile_indels -g /net/fantasia/home/atks/ref/vt/grch37/indel.reference.txt -r /net/fantasia/home/atks/ref/vt/grch37/hs37d5.fa run/final/all.genotypes.bcf -i 22:36000000-37000000 -f "PASS" |
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| data set | | data set |
| No Indels : 613 [0.72] | | No Indels : 613 [0.72] |
− | FS/NFS : 0.50 (2/2) | + | FS/NFS : 0.50 (2/2) #frame shift / non frameshift indels proportion, the bracket gives the counts of the frame shift and non frameshift indels |
− | Low complexity : 0.46 (283/613) <br> | + | Low complexity : 0.46 (283/613) #fraction of indels in low complexity region, the bracket gives the counts of the indels <br> |
− | 1000G | + | 1000G #1000 Genomes Phase 1 data set |
− | A-B 371 [0.76] | + | A-B 371 [0.76] #variants found in data set only |
− | A&B 242 [0.66] | + | A&B 242 [0.66] #variants found in both data sets |
− | B-A 276 [0.89] | + | B-A 276 [0.89] #variants found in 1000G phase 1 data set only |
− | Precision 39.5% | + | Precision 39.5% #39.6% of the call set are previously known, so 60.5% are novel variants. |
− | Sensitivity 46.7% <br> | + | Sensitivity 46.7% #sensitivity of variant calling, 46,7% of known variants from 1000 Genomes were rediscovered <br> |
− | mills | + | mills #Mills et al. data set |
| A-B 542 [0.68] | | A-B 542 [0.68] |
| A&B 71 [1.03] | | A&B 71 [1.03] |
| B-A 31 [1.07] | | B-A 31 [1.07] |
| Precision 11.6% | | Precision 11.6% |
− | Sensitivity 69.6% <br> | + | Sensitivity 69.6% <br> |
− | dbsnp | + | dbsnp # Indels from dbSNP |
| A-B 405 [0.68] | | A-B 405 [0.68] |
| A&B 208 [0.79] | | A&B 208 [0.79] |
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| * dbsnp: contains Indels submitted from everywhere, I am not sure what does this represent exactly. But assuming most are real, then precision is a useful estimated quantity from this reference data set. | | * dbsnp: contains Indels submitted from everywhere, I am not sure what does this represent exactly. But assuming most are real, then precision is a useful estimated quantity from this reference data set. |
| * Mills: contains doublehit common indels from the Mills. et al paper and is a relatively good measure of sensitivity for common variants. Because not all Indels in this set is expected to be present in your sample, this actually gives you an underestimate of sensitivity. | | * Mills: contains doublehit common indels from the Mills. et al paper and is a relatively good measure of sensitivity for common variants. Because not all Indels in this set is expected to be present in your sample, this actually gives you an underestimate of sensitivity. |
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| + | We perform the same analysis for the failed variants again: |
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| vt profile_indels -g /net/fantasia/home/atks/ref/vt/grch37/indel.reference.txt -r /net/fantasia/home/atks/ref/vt/grch37/hs37d5.fa run/final/all.genotypes.bcf -i 22:36000000-37000000 -f "~PASS" | | vt profile_indels -g /net/fantasia/home/atks/ref/vt/grch37/indel.reference.txt -r /net/fantasia/home/atks/ref/vt/grch37/hs37d5.fa run/final/all.genotypes.bcf -i 22:36000000-37000000 -f "~PASS" |
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| Precision 4.7% | | Precision 4.7% |
| Sensitivity 0.7% | | Sensitivity 0.7% |
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| This analysis supports filters too. | | This analysis supports filters too. |
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