Differences
This shows you the differences between two versions of the page.
|
bierapp_ex6 [2017/03/05 16:26] fgarcia |
bierapp_ex6 [2017/05/24 14:23] (current) |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| + | ====== Exercise 6====== | ||
| + | |||
| + | =====Data description: cases vs. controls ===== | ||
| + | |||
| + | \\ | ||
| + | {{:ex6.png?500|}} | ||
| + | \\ | ||
| + | \\ | ||
| + | =====Working plan===== | ||
| + | |||
| + | ====How many variants do you detect for each scenario?==== | ||
| + | ===A. Individual filters=== | ||
| + | - [[http://www.clcsupport.com/clcgenomicsworkbench/650/Variant_types.html|Description of variants]]. How many SNVs, INDELs, MNVs, SVs, CNVs? | ||
| + | - Reference for all controls and homozygous variant for all cases. | ||
| + | - Reference for all controls and heterozygous variant for all cases. | ||
| + | |||
| + | \\ | ||
| + | ===B. Progressive selection=== | ||
| + | |||
| + | - We have several clues about our candidate variants: | ||
| + | *Reference for all controls and heterozygous variant for all cases. | ||
| + | *We search variants with MAF < 0.001 (for all populations in 1000 Genomes phase 3) because it is a rare disease. | ||
| + | *Chromosome 13 | ||
| + | ***How many variants do you have including both characteristics?** | ||
| + | *Select this variant and visualize it from the Genomic browser. | ||
| + | \\ | ||
| + | \\ | ||
| + | /* | ||
| + | ====Solutions==== | ||
| + | Some of these solutions could be different when having updated databases | ||
| + | |||
| + | ===A. Individual filters=== | ||
| + | - 36424 SNVs, 3556 INDELs, 16 MNVs, 4 SVs, 0 CNVs | ||
| + | - Candidate variants: 0 | ||
| + | - Candidate variants: 2214 | ||
| + | |||
| + | |||
| + | ===B. Progressive selection=== | ||
| + | - 2214 -> 705 -> 1 | ||
| + | |||
| + | */ | ||