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1000 Genomes example

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fgardos edited this page Dec 31, 2013 · 19 revisions

BierApp includes an example based on 1000 Genomes data.

We generate a synthetic family consisting of 4 people: father (id: NA19661), mother (id: NA19660) son (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).

ped file

BierApp input:

A multi-sample VCF file.

Two steps:

  • Uploading multi-sample VCF file in BierApp.
  • After visualizing initial results you can use different filtering options to refine your variant selection strategy.

BierApp outputs:

  • 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

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