1,102
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSequencing Workshop Analysis of Indels (view source)
Revision as of 18:08, 15 June 2014
, 18:08, 15 June 2014→Peek
Time elapsed: 0.01s
Time elapsed: 0.01s
== Comparison with other data sets ==
Note that about 47% of the i
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
profile_indels v0.5
data set
No Indels : 720 [0.84] #720 indels, with and insertion deletion ratio of 0.84
FS/NFS : 0.50 (2/2) #only 4 variants overlap with coding regions, half of which are frameshift variants
Low complexity : 0.47 (335/720) #47% of the variants are in low complexity regions <br>
1000G
A-B 719 [0.83]
A&B 1 [inf] #only one variant overlaps with 1000 Genomes phase 1 data set.
B-A 517 [0.77]
Precision 0.1%
Sensitivity 0.2% <br>
mills
A-B 720 [0.84]
A&B 0 [-nan] #no variants overlaps with Mills et al. double hit variants.
B-A 102 [1.04]
Precision 0.0%
Sensitivity 0.0% <br>
dbsnp
A-B 720 [0.84]
A&B 0 [-nan] #no variants overlaps with Mills et al. double hit variants.
B-A 702 [1.52]
Precision 0.0%
Sensitivity 0.0%
This discovery set appears to have many novel variants! (or false positives)
==Peek==
==Peek==
