Usage

The querynator is used from the command line. Use the help function to display all options and choices.

querynator --help
querynator query-api-cgi --help

Quickstart

A typical command to query the cancergenomeinterpeter - CGI:

querynator query-api-cgi \
    -m mutations.[vcf,tsv,gtf] \
    -o sample_name \
    -g hg38 \
    -c 'Any cancer type' \
    --email your-cgi-account-mail@whatever.com \
    --token your-cgi-token

The command above downloads the following files from CGI. For further information please refer to their FAQ.

sample_name.cgi_results
├── drug_prescription.tsv
├── input01.tsv
├── metadata.txt
└── mutation_analysis.tsv

Mutation, CNA & translocation analysis

If you run the command with all possible input files, you will obtain:

# run command
querynator query-api-cgi \
    --mutations mutations.[vcf,tsv,gtf] \
    --cnas cnas.tsv \
    --translocations translocations.tsv \
    -o sample_name \
    -g hg38 \
    -c 'Any cancer type' \
    --email your-cgi-account-mail@whatever.com \
    --token your-cgi-token

# output
sample_name.cgi_results
├── cna_analysis.tsv
├── drug_prescription.tsv
├── fusion_analysis.tsv
├── input01.tsv
├── input02.tsv
├── input03.tsv
├── metadata.txt
└── mutation_analysis.tsv

Input file formats

For detailed information please refer to CGI formats. The genomic tabular format gtf is displayed below and contains partly the same columns as a vcf file (>v. 4.0) and is tab-separated. The sample column is not mandatory, but recommended when more than one sample is contained in one file.

A mutations/variant file can have the extensions vcf, tsv or gtf. The column names can also be uppercase letters as in a vcf.

mutations.[tsv,gtf]

sample	#chrom/chr	pos	ref	alt
test1	chr4	121369475	A	T
test2	chr10	122630837	C	G

A copy number alterations file should be tsv and column names must be lowercase.

cnas.tsv

sample	gene	cna
test1	ERBB2	amp
test2	TP53	del

A copy number alterations file should be tsv and column names must be lowercase.

translocations.tsv

sample	fus
test1	BCR__ABL1
test2	PML__RARA

Genome build versions

Note

The cancergenomeinterpeter will perform a liftover of the genomic coordinates to hg38 if the parameter --genome hg19 is used.