1000 Genomes example
BierApp includes an example based on 1000 Genomes data.
We generate a synthetic family consisting of 4 people: father (id: NA19661), mother (id: NA19660) are (id: NA19685) and daughter (id: NA19600). The first 3 people come from m008 trio in 1000 Genomes data.
It was created a VCF file for daughter including variants of X chromosome from the mother and the rest of chromosomes, the father and mother provided randomly 50% of the variants.
A multi-sample VCF file was prepared and 1000 variants of the family were randomly selected. Mother, father and son are unaffected. Daughter is affected, so it was included a mutation for her: TC / C in the position chr11: 61724448 (this deletion is causing a frame-shift).
A multi-sample VCF file.
- Uploading multi-sample VCF file in BierApp.
- After visualizing initial results you can use different filtering options to refine your variant selection strategy.
- Summary: global statistics and a graphical representation for consequence type.
- Variants and effects: detected variants and its effects for all samples.
- Genome viewer: selected variants can be visualized from this genome browser