Skip to content

Loading a case

Variants are loaded in a case context, this way it becomes possible to trace back where we have observed a variation. VCF files usually does not hold family information, this is why we use a ped file.

When loading a case for the first time one could do any of the following:

  1. Load a case with an SNV file
  2. Load a case with an SV file
  3. Load a case with an SNV file and an SV file

It is possible to add a file after a case is loaded with loqusdb update

A case is loaded with:

$loqusdb load --help
Usage: loqusdb load [OPTIONS]

  Load the variants of a case

  A variant is loaded if it is observed in any individual of a case If no
  family file is provided all individuals in vcf file will be considered.

Options:
  --variant-file <vcf_file>       Load a VCF with SNV/INDEL Variants
  --sv-variants <sv_vcf_file>     Load a VCF with Structural Variants
  -f, --family-file <ped_file>
  -t, --family-type [ped|alt|cmms|mip]
                                  If the analysis use one of the known setups,
                                  please specify which one.  [default: ped]
  -c, --case-id TEXT              If a different case id than the one in ped
                                  file should be used
  -s, --skip-case-id              Do not store case information on variants
                                  [default: False]
  --ensure-index                  Make sure that the indexes are in place
  --gq-threshold INTEGER           Threshold to consider variant  [default: 20]
  -m, --max-window INTEGER        Specify the maximum window size for svs
                                  [default: 2000]
  --check-profile PATH            Apply sample profiling for the samples,
                                  using the variants in this vcf
  --hard-threshold FLOAT          profile hamming distance to rejecting load
                                  (0-1)
  --soft-threshold FLOAT          profile hamming distance to store similar
                                  individuals (0-1)
  --help                          Show this message and exit.

Loqusdb will check that the individuals in ped file exists in vcf file and then add all the variants to database. If no .ped file is provided when loading a case in loqusdb, then variants for all samples found in the VCF file(s) will be loaded. In this case it will be necessary to provide a case name for this group of samples by using the --case-id option.

Command line example

A few demo files could be used to test a loqusdb instance. They are included in the tests folder, under fixtures.

To load all variants for a case by providing both a VCF file containing SNV variants and a VCF file containing SV variants, use the following command:

loqusdb --uri mongodb://<user>:<password>@<host>:<port> --database <database_name> --load --variant-file tests/fixtures/643594.clinical.vcf.gz --sv-variants tests/fixtures/643594.clinical.SV.vcf --case-id 643594

where 643594 in the command above is an arbitrary name assigned to the group of samples present in the VCF file.