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Updating case individuals tracks using the command line.

After a case is loaded and saved in the database, some individual-specific keys can be modified without having to re-upload the entire case. These key/values are relative to the optional tracks available for the individual and must be set at the individual level (each of them specified for each individual).

The command line command used to update individuals track is the following:

Usage: scout update individual [OPTIONS] [KEY] [VALUE]

  Update information on individual level in Scout

  UPDATE_DICT holds keys and type of value. If the value type is "path", and
  most are, a check for file existence is performed.

  If the key contains a dot (only one needed currently), keys for a dict type
  value is assumed: e.g. "reviewer.alignment" -> ind["reviewer"]["alignment"]
  (path value required)

Options:
  -c, --case-id TEXT  Case id  [required]
  -n, --ind TEXT      Individual display name
  --help              Show this message and exit.

And the tracks that can be updated are the following: - bam_file - d4_file - rna_alignment_path - mt_bam - vcf2cytosure - rhocall_bed - rhocall_wig - tiddit_coverage_wig - upd_regions_bed - upd_sites_bed - rna_coverage_bigwig - splice_junctions_bed

Additional sample descriptors: - subject_id - omics_sample_id

Additional non-track individual data - bionano_access - chromograph_images - reviewer

Description of custom individual tracks

DNA-sequencing alignment files

The following files are used by the igv.js integrated browser to display sequence variation alignments. The igv.js browser can be opened by clicking on the relative link (button) present on variants page. The link is displayed only if at least one individual of the case contains one bam_file or mt_bam track saved.

key name key value
bam_file path to a bam/cram alignment file
mt_bam path to a downsampled mitochondrial bam/cram alignment file
rhocall_bed path to rhocall output bed file
rhocall_wig path to rhocall output wig file
tiddit_coverage_wig path to tiddit wig coverage file
upd_regions_bed path to upd_regions_bed
upd_sites_bed path to vcf2cytosure file

rhocall_bed and rhocall_wig files are both obtained from rhocall, a software that calls and annotates autozygosity from VCF files.

tiddit_coverage_wig files are obtained from tiddit, a software which in turn is used to call structural variants.

upd_regions_bed and upd_sites_bed files are created from VCF files using the upd tool.

RNA-sequencing splice junctions files

These files are both required by the integrated splice junction track view of igv.js.

key name key value
splice_junctions_bed path to An indexed junctions .bed.gz file obtained
rna_coverage_bigwig path to coverage islands file generated from bam or cram files

splice_junctions_bed is obtained from from STAR v2 aligner *.SJ.out.tab file and rna_coverage_bigwig contains coverage islands obtained from RNA-seq bam or cram alignments

A link to the splice junction view is present on variants pages of cases with at least one individual with these files.

vcf2cytosure file

key name key value
vcf2cytosure path to vcf2cytosure file

vcf2cytosure is a tool that converts a VCF with structural variations to the “.CGH” format used by the commercial CytoSure Interpret Software by OGT (Oxford Gene Technology). Once the individual is updated with this track, vcf2cytosure files will be available for download from the individuals table present on Scout's case page.

Sample identifiers

key name key value
subject_id Individual id for matching multiomics data and statistics
omics_sample_id Individual id for matching multiomics data and statistics

Subject ids are unique identifiers (eg as produced by a hospital LIMS) denoting individuals, who may have multiple samples in Scout. Useful for individual level statistics and connecting multiomics data or multiple analyses and cases including the same individual, potentially with different samples.

Omics sample ids can also be directly set. These correspond to the sample ids found in OMICS variant files, and directly identify the individual to whom the OMICS sample belongs. Useful for e.g. loading a combined DNA and RNA case.

Additional individual data - structured dictionary input

If the key contains a dot (only one needed currently), keys for a dict type value is assumed: e.g. "reviewer.alignment" -> ind["reviewer"]["alignment"].

BioNano Access

key name key value
bionano_access.sample BioNano Sample ID
bionano_access.project BioNano Project

See BioNano Access Integration.

Chromograph

key name key value
chromograph_images.autozygous Path wildcard to files - exclude chromosome name
chromograph_images.coverage Path wildcard to files - exclude chromosome name
chromograph_images.upd_regions Path wildcard to files - exclude chromosome name
chromograph_images.upd_sites Path wildcard to files - exclude chromosome name
See e.g. User guide - Cases - Cytogenomics for a description of Chromograph.

Scout REViewer Service

key name key value
reviewer.alignment Path
reviewer.alignment_index Path
reviewer.vcf Path
reviewer.catalog Path

See Admin guide - Scout REViewer Service for details on SRS.