Differences

This shows you the differences between two versions of the page.

Link to this comparison view

bierapp_ex3 [2016/09/27 16:14]
fgarcia
bierapp_ex3 [2017/05/24 14:23] (current)
Line 1: Line 1:
 +=====Data description=====
  
 +\\ 
 +{{:ex3.png?nolink|}}
 +\\
 +\\
 +=====Working plan=====
 +We have several candidate profiles of mutations because it is clear the kind of mutation we are searching but sometimes we do not have a specific clues.  
 +
 +====How many variants do you detect for each scenario?====
 +===A. Individual filters===
 + 
 +  - Recessive heritage
 +  - Dominant heritage (mother is affected).  
 +  - For these region, only chromosome: 3,19
 +  - Evaluate the same regions, including start and end at the first region:  3:1000-200000,19
 +  - For this gene: SDC3  
 +  - [[http://www.clcsupport.com/clcgenomicsworkbench/650/Variant_types.html|Description of variants]]. How many SNVs, INDELs, MNVs, SVs, CNVs?
 +  - Variants with  MAF (Minimum Allelic Frequency)   < 0.05 for AFR populations in 1000 Genomes phase 1
 +  - Variants with  MAF (Minimum Allelic Frequency)   < 0.05 for AFR populations in 1000 Genomes phase 3
 +  - Variants with  MAF (Minimum Allelic Frequency)   < 0.05 for African American population  in ESP 6500
 +  - For sift<0.05 and polyphen >0.95, because it is likely pathogenic
 +
 +\\
 +===B. Progressive selection===
 +
 +  - Can you apply filters to search "Insuline Resistance" phenotype in recesive heritage? 
 +
 +\\
 +\\
 +/*
 +====Solutions====
 +===A. Individual filters===
 +  - Candidate variants:  964
 +  - Candidate variants: 10852
 +  - Candidate variants:  5015
 +  - Candidate variants: 975
 +  - Candidate variants:  2
 +  - 36307 SNVs, 3666 INDELs, 23 MNVs, 3 SVs, 0 CNVs
 +  - Candidate variants in 1000 Genomes, phase 1: 16102
 +  - Candidate variants in 1000 Genomes, phase 3: 17468
 +  - Candidate variants in European American population: 24460
 +  - Candidate variants: 313
 +
 +===B. Progressive selection===
 +  - sift<0.05, polyphen>0.95, AFR phase3 < 0.1
 +
 +*/