Bedgovcf

BedGoVcf is a simple tool to dynamically convert BED files to VCF files using a YAML configuration file.

Usage

bedgovcf --bed <input.bed> --config <config.yaml> --fai <reference.fai>

Required Arguments

Argument	Description
--bed <path>	Path to the BED file to convert
--config <path>	Path to the YAML configuration file
--fai <path>	Path to the FASTA index file of the reference genome

Optional Arguments

Argument	Description
--output <path>	Path to the output VCF file (default: stdout)
--skip <integer>	Skip the first N lines of the BED file (default: 0)
--header	The BED file has a header (default: false)
--sample <string>	Sample name to use in the VCF file (default: prefix of the BED file)

The configuration file

The configuration file can be used to tell bedgovcf how to handle the BED file. It is a YAML file with the following structure:

⚠️ All names should be lowercase, otherwise the tool won't recognize them. ⚠️

# Optional headers to add to the VCF file
header:
  - name: header_name # The name of the header
    content: this header does something # The content of the header
  - name: other_header_name
    content: this header does something else

# Optional chromosome field (will default to the first column of the BED file)
chrom:
  value: $0 # The value to use for the chromosome field
  prefix: chr # A prefix to add to the chromosome field

# Optional position field (will default to the second column of the BED file)
pos:
  value: $1 # The value to use for the position field

# Optional ID field (will default to an incrementing number)
id:
  value: $5 # The value to use for the ID field
  prefix: toolname_ # A prefix to add to the ID field

# Optional reference field (will default to N)
ref:
  value: "N" # The value to use for the reference field

# Optional alternate field (will default to <CNV>)
alt:
  value: ~if $4 < 0 <DEL> <DUP> # The value to use for the alternate field
  options: # All possibilities for the alternate field
    - name: DEL
      description: Deletion
    - name: DUP
      description: Duplication

# Optional quality field (will default to '.')
qual:
  value: $6 # The value to use for the quality field

# Optional filter field (will default to PASS)
filter:
  value: ~if $6 >= 0 PASS LOWQUAL # The value to use for the filter field
  options: # All possibilities for the filter field
    - name: PASS
      description: Passed all filters
    - name: LOWQUAL
      description: Low quality

# Optional info fields (will default to no info fields)
# These are some examples, but you can add whatever fields you want
info:
  - name: SVTYPE # The name of the info field
    value: ~if $4 < 0 DEL DUP # The value to use for the info field
    number: 1 # The number of values for the info field
    type: String # The type of the info field
    description: Type of structural variant # The description of the info field
  - name: SVLEN
    value: ~min $2 $1
    number: 1
    type: Integer
    description: Length of structural variant
  - name: END
    value: $2
    number: 1
    type: Integer
    description: End position of structural variant

# Optional format fields (will default to no format fields)
# These are some examples, but you can add whatever fields you want
format:
  - name: GT # The name of the format field
    value: ~if $4 < 0 0/1 1/1 # The value to use for the format field
    number: 1 # The number of values for the format field
    type: String # The type of the format field
    description: Genotype of the sample # The description of the format field
  - name: CN
    value: ~round $4
    number: 1
    type: Integer
    description: Copy number of the sample

Dynamically fetching fields from the BED file

All value fields in the config can be resolved by column names. For example, if you have a BED file with the following columns:

start	end	chromosome
1	2	chr1

You can use the following config to resolve the chrom and pos fields (when using the --header option):

chrom:
  value: $chromosome
pos:
  value: $start

When no header is present you can also use the 0-based index of the column like this:

chrom:
  value: $2
pos:
  value: $0

Functions

The value fields in the config can also be resolved by using functions (words starting with ~). The following functions are available:

~round

Pattern: ~round <value>

Rounds the given value to the nearest integer.

⚠️ This function will panic if the given value is not an integer or a float. ⚠️

~sum

Pattern: ~sum <value1> <value2> ...

Adds all values together.

⚠️ This function will panic if the given values are not integers or floats. ⚠️

~min

Pattern: ~min <value1> <value2> ...

Substracts all values from the first value.

⚠️ This function will panic if the given values are not integers or floats. ⚠️

~if

Pattern: ~if <value1> <operator> <value2> <value_if_true> <value_if_false>

Checks if the given condition (<value1> <operator> <value2>) is true for the given values. If it is true, the value_if_true will be returned, otherwise the value_if_false will be returned. value_if_false can also be a new function (this way you can create nested if statements).

Supported operators: <, <=, >, >=, ==, !=

Installation

Mamba/Conda

This is the preffered way of installing BedGoVcf.

mamba install -c bioconda bedgovcf

or with conda:

conda install -c bioconda bedgovcf

Precompiled binaries

Precompiled binaries are available for Linux and macOS on the releases page.

Installation from source

Make sure you have go installed on your machine (or install it if you don't currently have it)

Then run these commands to install bedgovcf:

go get .
go build .
sudo mv bedgovcf /usr/local/bin/

Next run this command to check if it was correctly installed:

bedgovcf --help