1,102
edits
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Revision as of 15:42, 16 June 2014
, 15:42, 16 June 2014→Comparison with other data sets
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.
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
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"
data set
data set
No Indels : 720 [0.84] #720 indels, with and insertion deletion ratio of 0.84
No Indels : 613 [0.72]
FS/NFS : 0.50 (2/2) #only 4 variants overlap with coding regions, half of which are frameshift variants
FS/NFS : 0.50 (2/2)
Low complexity : 0.47 (335/720) #47% of the variants are in low complexity regions <br>
Low complexity : 0.46 (283/613) <br>
1000G
1000G
A-B 719 [0.83] #value in brackets is the insertion deletion ratio
A-B 371 [0.76]
A&B 1 [inf] #only one variant overlaps with 1000 Genomes phase 1 data set.
A&B 242 [0.66]
B-A 517 [0.77]
B-A 276 [0.89]
Precision 0.1%
Precision 39.5%
Sensitivity 0.2% <br>
Sensitivity 46.7% <br>
mills
mills
A-B 720 [0.84]
A-B 542 [0.68]
A&B 0 [-nan] #no variants overlaps with Mills et al. double hit variants.
A&B 71 [1.03]
B-A 102 [1.04]
B-A 31 [1.07]
Precision 0.0%
Precision 11.6%
Sensitivity 0.0% <br>
Sensitivity 69.6% <br>
dbsnp
dbsnp
A-B 720 [0.84]
A-B 405 [0.68]
A&B 0 [-nan] #no variants overlaps with Mills et al. double hit variants.
A&B 208 [0.79]
B-A 702 [1.52]
B-A 494 [2.03]
Precision 0.0%
Precision 33.9%
Sensitivity 0.0%
Sensitivity 29.6%
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.
* 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.
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"
data set
No Indels : 107 [2.06]
FS/NFS : -nan (0/0)
Low complexity : 0.79 (85/107) <br>
1000G
A-B 107 [2.06]
A&B 0 [-nan]
B-A 518 [0.77]
Precision 0.0%
Sensitivity 0.0% <br>
mills
A-B 105 [2.09]
A&B 2 [1.00]
B-A 100 [1.04]
Precision 1.9%
Sensitivity 2.0% <br>
dbsnp
A-B 102 [2.00]
A&B 5 [4.00]
B-A 697 [1.51]
Precision 4.7%
Sensitivity 0.7%
This analysis supports filters too.
This analysis supports filters too.
