2.13. Loading VCF files

The first column of a VCF file is the reference sequence ID. In order to load a VCF file, it’s required to have a reference FASTA file loaded.

The VCF file must be indexed using tabix.

2.13.1. Load VCF

python manage.py load_vcf --file organism_snv_sorted.vcf.gz --organism 'Arabidopsis thaliana'

• Loading this file can be faster if you increase the number of threads (–cpu).

python manage.py load_vcf --help

–file	VCF genome file indexed with tabix (see http://www.htslib.org/doc/tabix.html) *
–organism	Species name (eg. Homo sapiens, Mus musculus) *
–doi	DOI of a reference stored using load_publication (eg. 10.1111/s12122-012-1313-4)
–cpu	Number of threads

* required fields

2.13.2. Remove file

If, by any reason, you need to remove a VCF dataset you should use the command remove_file. If you delete a file, every record that depend on it will be deleted on cascade.

python manage.py remove_file --help

• This command requires the file name (Dbxrefprop.value)