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bierapp_ex1 [2017/03/05 16:25]
fgarcia 		bierapp_ex1 [2017/05/24 14:23] (current)
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 +=====Data description=====
  
 +\\ 
 +{{:ex1.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 this region: 1:1000-50000
 +  - For this gene: BRD9
 +  - For these genes at the same time: BRD9,CDK11A,RET
 +  - [[http://www.clcsupport.com/clcgenomicsworkbench/650/Variant_types.html|Description of variants]]. How many SNVs and INDELs can you search?
 +  - Variants with  MAF (Minimum Allelic Frequency)   < 0.1 for all populations in 1000 Genomes phase 3 
 +  - Variants with  MAF (Minimum Allelic Frequency)   < 0.01 for all populations in 1000 Genomes phase 3 
 +  - Variants with  MAF (Minimum Allelic Frequency)   < 0.001 for all populations in 1000 Genomes phase 3
 +\\
 +===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 "synonymous variant"  
 +      ***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 "synonymous variant"  
 +      ***How many variants do you have including both characteristics?**
 +
 +\\
 +\\
 +/*
 +====Solutions====
 +Some of these solutions could be different when having updated  databases
 +
 +===A. Individual filters===
 +  - Candidate variants:  1312
 +  - Candidate variants:  10722
 +  - Candidate variants:  1
 +  - Candidate variants: 9
 +  - Candidate variants:  34
 +  - 39980 SNVs and INDELs
 +  - Candidate variants in 1000 Genomes, phase 3:17333
 +  - Candidate variants in 1000 Genomes, phase 3:13190
 +  - Candidate variants in 1000 Genomes, phase 3:12270
 +
 +===B. Progressive selection===
 +  - 1312-449-46
 +  - 10722-5171-655
 +
 +*/