Differences

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

Link to this comparison view

bierapp_ex2 [2016/09/27 16:02]
fgarcia 		bierapp_ex2 [2017/05/24 14:23] (current)
Line 1: Line 1:
 +=====Data description=====
 +
 +\\ 
 +{{:ex2.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 (father is affected).  
 +  - For these regions: 1:3000-10000000,20:1000-200000000
 +  - For these genes: CDK11A,CDK11B  
 +  - Are there variants for this SNPId: rs17279437?
 +  - [[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)   < 0.001 for EUR populations in 1000 Genomes phase 3
 +  - Variants with  MAF (Minimum Allelic Frequency)   < 0.001 for EAS populations in 1000 Genomes phase 3
 +  - Variants with two preview MAFs at the same time
 +
 +\\
 +===B. Progressive selection===
 +
 +   - We have several clues about our candidate variants. In addition of  knowing the pattern of recessive heritage, we search variants with MAF < 0.1  (for all populations in 1000 Genomes phase 3) because it is a rare disease. Consequence type must be "non coding exon variant" (**modifier**).  
 +      ***How many variants do you have including both characteristics?**
 +   - We have several clues about our candidate variants. In addition of  knowing the pattern of dominant heritage (father is affected), we search variants with MAF < 0.1  (for all populations in 1000 Genomes phase 3) because it is a rare disease. Consequence type must be "non coding exon variant" (**modifier**). 
 +      ***How many variants do you have including both characteristics?**
 + /*   ***Download these final results in a csv file**
 +
 +
 +\\
 +\\
 +====Solutions====
 +===A. Individual filters===
 +  - Candidate variants:  1729
 +  - Candidate variants:  6229
 +  - Candidate variants: 1309
 +  - Candidate variants: 19
 +  - Candidate variants: 1
 +  - 36440 SNVs, 3538 INDELs, 19 MNVs, 2 SVs, 0 CNVs
 +  - Candidate variants in EUR 1000 Genomes, phase 3: 12346
 +  - Candidate variants in EAS 1000 Genomes, phase 3: 15217
 +  - Candidate variants in the three MAFs: 12292
 +
 +===B. Progressive selection===
 +  - 1729-541-116
 +  - 6229-2878-699
 +
 +
 +*/