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.] |
-a
--auto-create |
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] |
--no-autodetect |
do not auto-link properties with tsv columns based on identical names [opt] |
--no-update |
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 |
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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] |
--default |
specify default value [opt] |
sonar delete-prop |
delete property |
--db FILE |
specify name of the database |
--name STR |
specify new property name |
--force |
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] |
--PROP VALUE [VALUE, ...] |
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 |
--showNX |
show uninformative variant allels for genome profiles [opt] |
--out-cols STR [STR, ...] |
specify columns to show (for tsv and csv only) [opt] |
--count |
show number of matching genomes only [opt] |
--format {csv, tsv, vcf} |
specify the output format [opt] |
-o FILE
--out FILE |
write output to the given file [opt] |
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Mutation Notations
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Genome level |
Protein level |
Substitution |
REFposALT
e.g. A3451T |
PROT:REFposALT
e.g. A3451T |
Insertion |
REFposALT
e.g. A4057TGAT |
PROT:REFposALT
e.g. N:A34AK |
1-bp Deletion |
del:pos
e.g. del:11288 |
PROT:del:pos
e.g. ORF1ab:del:300 |
multi-bp Deletion |
del:start-end
e.g. del:112-115 |
PROT:del:start-end
e.g. S:del:68-69 |
Deletion with fixed coordinates |
del:=start-=end
e.g. del:=8-=11 |
PROT:del:=start-=end
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
integer |
for storing integers |
float |
for storing decimal numbers |
text |
for storing strings |
dates |
for storing dates in the form YYYY-MM-DD |
zip |
for storing zip codes |
Operators for Data Types
Operator |
Description |
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.
2021-01-01:2021-12-31) |
integer, float, date |
^ |
not the same as (e.g. ^B.1.1.7) |
text |
% |
wildcard standing for any character(s) (e.g. %human%) |
text |
Make sure that expressions with > or < are quoted to prevent misinterpretation by the shell
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