ktym / vcftobeacon

vcftobeacon

A script to convert VCF files into GA4GH Beacon database files for PostgreSQL with the help of bcftools.

Prerequisites

• bcftools with a +fill-tags plugin
  • try bcftools +fill-tags -vv to see if you have the plugin
• Ruby 1.8 or later

Usage

% ruby vcftobeacon.rb /path/to/*.vcf > vcftobeacon.log

Options

You can supply options via environmental/shell variables.

% BeaconDatasetID=5 BeaconDataSeparator=";" BeaconChrsFile=/path/to/conv_file.txt BeaconDataHeader=true ruby vcftobeacon.rb /path/to/*.vcf > vcftobeacon.log

Or you can override default values and environmental/shell variables by the command line options.

% ruby vcftobeacon.rb -i 123 -s ";" -c /path/to/conv_file.txt -p /path/to/*.vcf > vcftobeacon.log

Each option has a longer form as well.

% ruby vcftobeacon.rb --datasetid 123 --separator ";" --chrsfile /path/to/conv_file.txt --header /path/to/*.vcf > vcftobeacon.log

Note that the command line options override the environmental/shell variables.

Dataset ID

To change the dataset ID,

• set the environmental/shell variable BeaconDatasetID
• or use the option --datasetid / -i
• (deafult: 1)

Column separator

To change the separator (delimiter) of columns, e.g., change to ";" for SQL,

• set the environmental/shell variable BeaconDataSeparator
• or use the option --separator / -s
• (default: "\t")

Column headers

To print column headers,

• set the environmental/shell variable BeaconDataHeader to any value, e.g., "true"
• or use the option --header / -p with no argument
• (default: false)

Rename chromosome names

To change the file to rename chromosomes,

• set the environmental/shell variable BeaconChrsFile
• or use the option --chrsfile / -c
• (default: "./chr_name_conv.txt")

Sample columns

If your VCF doesn't contain sample columns, skip +fill-tags

• use the option nofilltags / -n

Authors

• Toshiaki Katayama [e-mail] (Database Center for Life Science, Chiba, Japan)
• Dietmar Fernandez-Orth [e-mail] (Centre for Genomic Regulation, Barcelona, Spain)

License

• MIT

TODO

Couldn't make the first autoincrement id column to null in data; if it's possible, we could use the following shortcut, hopefully:

% cat file | psql -h localhost -p 5432 -d elixir_beacon_dev -U microaccounts_dev -c "copy beacon_data_table from stdin with (format 'text')"