BGEN file - Githubissues

rivas-lab / nanopore

Tools for analysis of long-read sequencing data.

0 stars 0 forks source link

BGEN file #3

Closed yk-tanigawa closed 7 years ago

yk-tanigawa commented 8 years ago

Understand the BGEN file format
Be able to manipulate haplotype reference data stored in BGEN file.
- extract the region of interest, etc..

yk-tanigawa commented 8 years ago

Things to discuss with Chris

C++ library to represent haplotypes
a piece of code to read/write BGEN file
- how to select the specific regions of the genome

yk-tanigawa commented 8 years ago

Ask Chris for PINK2 code

yk-tanigawa commented 7 years ago

Gavin Band’s bitbucket:

https://bitbucket.org/gavinband/bgen
- https://bitbucket.org/gavinband/bgen/src/e684677041f15c26fd310b67cce6b6ad50c49e84/example/bgen_to_vcf.cpp?at=default&fileviewer=file-view-default

yk-tanigawa commented 7 years ago

“Imputed data is delivered in bgen format, and around 5TB of storage would be required to download the entire imputed data on 500,000 participants (the imputed dataset on the first 150,000 participants is just under 1.5TB). The information scores that correspond to the quality measure of the imputed genotypes have been computed with QCTOOL and can be downloaded from the Resources tab on a per Chromosome basis as part of the Imputed minor allele frequencies datasets.”

http://www.well.ox.ac.uk/~gav/bgen_format/

yk-tanigawa commented 7 years ago

We have decided to use pgen instead of bgen, so I am closing this ticket.