reference-annotations

Makefile for building .bed formatted reference annotation files for hg19 human genome genes & genomic regions

Usage

First, clone this repository and change to its directory:

git clone https://github.com/stevekm/reference-annotations.git
cd reference-annotations

Generate the desired annotation files; either gencode, ensembl, or all for both Gencode and Ensembl.

make all

# or

make gencode

# or

make ensembl

Output

The following files are created:

• gencode.v19.annotation.genes.bed: Gencode hg19 gene annotations & genomic regions

• Homo_sapiens.GRCh37.82.noGLMT.chr.genes.bed: Ensembl hg19 gene annotations & genomic regions, with the following modifications:

  • removed file comments

  • removed entries with 'MT' listed for chromosome

  • removed entries with 'GL....' listed for chromosome, e.g. 'GL000229.1'

  • added 'chr' to the start of all chromosome labels

Notes

Intermediate files are removed by default. If you want to keep them, then comment out the .INTERMEDIATE section in the Makefile.

Software

• GNU make

• BEDOPS

Resources

Gencode Releases: https://www.gencodegenes.org/releases/