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bierapp_ex5 [2017/05/24 11:26] (current)
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 +====== Exercise 5======
  
 +=====Data description=====
 +
 +\\ 
 +{{:ex5.png?500|}}
 +\\
 +\\
 +=====Working plan=====
 +We have several candidate profiles of mutations to explore:
 +
 +====How many variants do you detect for each scenario?====
 +===A. Individual filters===
 + 
 +  - Recessive heritage
 +  - Dominant heritage (mother is affected).
 +  - For chromosomes 1 and 3
 +  - Evaluate these regions at the same time:  1:10000-500000, 11:1000-500000, 13:500-100000
 +  - For theses genes: BRCA1,BRCA2
 +  - Are there variants for these SNPs: rs6682385,rs75478250,rs147502335,rs368140013,rs7951297?
 +  - [[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)   < 0.005 for Asian population in 1000 Genomes phase 1
 +  - Variants with  MAF (Minimum Allelic Frequency)   < 0.005 for East Asian population in 1000 Genomes phase 3
 +  - Variants with  MAF (Minimum Allelic Frequency)   < 0.005 for South Asian population in 1000 Genomes phase 3
 +
 +\\
 +===B. Progressive selection===
 +
 +  - There are clear information about our candidate variants:
 +    *Recessive heritage 
 +    *Chromosomes 5 and 7
 +    *INDEL
 +      ***How many variants do you have including both characteristics?**
 +      ***Download these final results in a csv file**
 +  - We have other interesting scenario where we are sure there are several candidate variants:
 +    *Heterozygous variant for mother and daughter and father is reference (0/0)
 +    *Consequence type: "stop lost"
 +    *We search new variants without rs ID 
 +    *BiERapp includes details about "Genomic context", "Pop. Frequencies", "Phenotype" and "Effect". Please, could you explain a bit this information?
 +
 +/*
 +
 +\\
 +\\
 +====Solutions====
 +===A. Individual filters===
 +  - Candidate variants: 1688 
 +  - Candidate variants: 6084
 +  - Candidate variants: 6459
 +  - Candidate variants: 60 
 +  - Candidate variants: 13 
 +  - Candidate variants: 1
 +  - 36385 SNVs, 3596 INDELs, 13 MNVs, 4 SVs, 0 CNVs
 +  - Candidate variants in 1000 Genomes, phase 1: 14948
 +  - Candidate variants in 1000 Genomes, phase 3: 15730
 +  - Candidate variants in European American population: 13029
 +
 +===B. Progressive selection===
 +  - 1688 -> 164 -> 20
 +  - 4432 -> 2 -> 1
 +
 +*/