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covSonar 2 Cheat Sheet by

A quick reference guide for genomic profiling using covSonar (

Database Setup

sonar setup
--db FILE
specify the name of the new database
--gbk FILE
set a custom reference based on the specified Genbank file [opt.]
add pre-de­fined sample properties to the new database [opt.]

Show Infos

sonar info
--db FILE
specify name of the database

Sample Management

sonar import
to import data
--db FILE
specify name of the database
--fasta FILE [FILE, ...]
specify fasta file to import sequences [opt]
--tsv FILE [FILE, ...]
specify tab-de­limited text file to import meta inform­ation [opt]
--cols STR [STR, ...]
link properties with tsv columns in the form of
prop_n­ame­=co­l_h­eader [opt]
do not auto-link properties with tsv columns based on identical names [opt]
skip data of existing samples [opt]
--cache DIR
specify a folder to cache import data [opt]
-t INT
--threads INT
specify number of threads / cpus to use [opt]
sonar delete
to delete sample(s)
--db FILE
specify name of the database
--sample STR [STR, ...]
specify names of samples to delete [opt]
--sample-file FILE
specify file containing names of samples to delete [opt]
--force FILE
force deletion and skip user confir­mation [opt]
sonar optimize
}to clean database
--db FILE
specify name of the database
sonar db-upgrade
upgrade database to the latest version
--db FILE
specify name of the database

Property Management

sonar list-prop
to list available properties
--db FILE
specify name of the database
sonar add-prop
add new property
--db FILE
specify name of the database
--name STR
specify new property name matching to [A-Z][­A-Z­0-9_]+
--descr STR
provide a short property descri­ption
--dtype STR
specify data type
--qtype STR
specify query type [opt]
specify default value [opt]
sonar delete-prop
delete property
--db FILE
specify name of the database
--name STR
specify new property name
force deletion without user confir­mation [opt]

Query Genomes

sonar match
--sample STR [STR, ...]
consider given samples only [opt]
--sample-file *FILE
consider samples listed in the given file only [opt]
--profile STR [STR, ...]
match given mutation profile (use argument multiple times to define alternate profiles) [opt]
filter based on sample property (PROP has to be replaced by the actual property name) [opt]
--with-sublineage PROP
include pangolin sub-li­neages for the given property [opt]
Use sonar update­-li­nea­ge-info to update lineage info before
show uninfo­rmative variant allels for genome profiles [opt]
--out-cols STR [STR, ...]
specify columns to show (for tsv and csv only) [opt]
show number of matching genomes only [opt]
--format {csv, tsv, vcf}
specify the output format [opt]
--out FILE
write output to the given file [opt]

Mutation Notations

Genome level
Protein level
e.g. A3451T
e.g. A3451T
e.g. A4057TGAT
e.g. N:A34AK
1-bp Deletion
e.g. del:11288
e.g. ORF1ab­:de­l:300
multi-bp Deletion
e.g. del:11­2-115
e.g. S:del:­68-69
Deletion with fixed coordi­nates
e.g. del:=8-=11
e.g. S:del:­=68-=69
Any notation can be negated by a preceding caret (^), e.g. ^A1345G only matches target genomes not carrying this SNP.
REF: reference allele; ALT: variant allele; pos: reference position (1-based); start and end: start and end reference coordi­nates (1-based); PROT: protein symbol

Data Types for Properties

for storing integers
for storing decimal numbers
for storing strings
for storing dates in the form YYYY-MM-DD
for storing zip codes

Operators for Data Types

Valid data type
larger than (e.g. >1)
integer, float, date
smaller than (e.g. <1)
integer, float, date
larger than or equal to (e.g. >=1)
integer, float, date
smaller than or equal to (e.g. <=1)
integer, float, date
different than (e.g. !=1)
integer, float, date
from:to range (e.g.
integer, float, date
not the same as (e.g. ^B.1.1.7)
wildcard standing for any charac­ter(s) (e.g. %human%)
Make sure that expres­sions with > or < are quoted to prevent misint­erp­ret­ation by the shell


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