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bierapp_ex2 [2016/09/27 16:02] fgarcia |
bierapp_ex2 [2017/05/24 14:23] (current) |
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+ | =====Data description===== | ||
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+ | {{:ex2.png?nolink|}} | ||
+ | \\ | ||
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+ | =====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** | ||
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+ | \\ | ||
+ | \\ | ||
+ | ====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 | ||
+ | |||
+ | |||
+ | */ | ||