ilarsf / MapDbSNP

Add positions to data that only contains dbSNP IDs

MapDbSNP

• UNIX commands and Rscripts will add positions to data that only contains dbSNP IDs
• Will download dbSNP151 from UCSC genome browser and prepare files for future runs (~90 GB hard disk space)

Required R packages

• data.table
• optparse
• parallel
• here

Usage

Rscript ./script/positionsFromDBSNP.r [options]

Options:

--input=path to file with dbSNP IDs, e.g. summary statistics
--ID=column name with dbSNP IDs
--build=Genome Build: hg19 or hg38
--outdir=Path of output directory
--prefix=Prefix for output file name without path or extension
--cpus=Number of available CPUs for parallel runs (uses up to 64 for hg19 or 68 for hg38)
--skip=Skip lines of input file

Example command line:

Rscript ./script/positionsFromDBSNP.r \
--input=./example/example_input.txt \
--ID=ID \
--build=hg19 \
--outdir=./example \
--prefix=example \
--cpus=16