cgivar2gvcf

Conversion of Complete Genomics var file to gVCF

This conversion assumes that the genome file is build 37 and does not currently support other builds.

Installation

This is Python package in the Python Package Index (PyPI). You can install it with pip install cgivar2gvcf. This installation will also install the twobitreader package.

Command line usage

You can run this tool on the command line like this:

python -m cgivar2gvcf -h

The above command will display the program's options.

Notably, you need to build a "build 37" 2 bit reference exact same with Complete Genomics Incorporated (CGI). You can refer to the dockerfile in cgatools-build37-crr to build a "build 37 fasta", and then cover it to 2bit fasta with faToTwoBit tool from UCSC

An example command for a variant-only VCF file (not gVCF):

python -m cgivar2gvcf -d files/ -i var-GS00253-ASM.tsv.bz2 --var-only -o GS00253-vcf-from-var.vcf.bz2

Module usage

convert_to_file

Writes the new VCF file to the specified output destination.

convert_to_file(cgi_input, output_file, twobit_ref, twobit_name, var_only=False)

• cgi_input - Inputed Complete Genomics var file. Can be a file-like object (i.e. already open) or a path to a file (uncompressed, gzip, or bzip2 compressed).
• output_file - Where to put the result. A "gz" suffix results in gzip compression, a "bz2" suffix results in bzip2 compression.
• twobit_ref - Path to the UCSC twobit reference genome file
• twobit_name - name of the twobit reference file (so we can cite this in the VCF header as the "reference")
• var_only - (optional) default false. Set to true if you only want variant lines.

convert

Returns a generator object that yields lines of the VCF file.

convert(cgi_input, twobit_ref, twobit_name, var_only=False)

• cgi_input - Inputed Complete Genomics var file. Can be a file-like object (i.e. already open) or a path to a file (uncompressed, gzip, or bzip2 compressed).
• twobit_ref - Path to the UCSC twobit reference genome file
• twobit_name - name of the twobit reference file (so we can cite this in the VCF header as the "reference")
• var_only - (optional) default false. Set to true if you only want variant lines.

get_reference_genome_file

Convenience function for finding the UCSC reference genome in a specified directory, and downloading it if it's not present.

get_reference_genome_file(refseqdir, build)

• refseqdir - The directory that should have the 2bit file (it will be downloaded to this directory if not already present)
• build - The genome build. There is currently only one option: build 37. (You can use 'b37'.) It's here so we can be explicit about this.