Awesome
SVDB
SVDB is a toolkit for constructing and querying structural variant databases. The databases are constructed using the output vcf files from structural variant callers such as TIDDIT, Manta, Fermikit or Delly. SVDB may also be used to merge SV vcf files from multiple callers or individuals.
Supported public databases
SVDB query supports public databases such as thousand genomes SV map and Gnomad SV, as well as most multisample SV vcf files
The thousand genomes SV database:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/
The swegen SVDB:
The GNOMAD SV database:
https://storage.googleapis.com/gnomad-public/papers/2019-sv/gnomad_v2_sv.sites.vcf.gz
external databases are run like this:
svdb --query \
--query_vcf /home/jesper/vcf/6_pair_limit/P2109_120.clean.dedup.recal_FindSV.vcf \
--out_occ GNOMAD_AC \
--out_frq GNOMAD_AF \
--in_occ AN \
--out_frq AF \
--db /home/jesper/Downloads/gnomad_sv/gnomad_v2_sv.sites.vcf
here the AF and AN are the allele frequency tags of the database, the AF is a float, and AN is an integer. These tags will be added to the annotated output vcf, and named GNOMAD_AC, GNOMAD_AF.
Install:
Dependencies: SVDB has been tested on python 2.7.11 and python 3.6, and requires numpy. SVDB is installed using the following command
git clone https://github.com/J35P312/SVDB.git
cd SVDB
pip install -e .
SVDB is available on singularity:
singularity pull shub://J35P312/SVDB
Modules:
SVDB consists of modules that are used to build, query, export, and analyse structural variant databases. These are the modules:
Build
This module is used to construct structural variant databases from vcf files. The database may then be queried to compute the frequency of structural variants, or exported into a vcf file. These are the commands used to construct a structural variation database:
print a help message
svdb --build --help
Construct a database, from a set of vcf files:
svdb --build --vcf sample1.vcf sample2.vcf sample3.vcf
construct a database from vcf files stored in a folder
svdb --build --folder SV_analysis_folder/
optional arguments:
-h, --help show this help message and exit
--files [FILES [FILES ...]] create a db using the specified vcf files(cannot be
used with --folder)
--folder FOLDER create a db using all the vcf files in the folders
--prefix PREFIX the prefix of the output file, default = SVDB
Export
This module is used to export the variants of the SVDB sqlite database. The variants of the sqlite svdb database is clustered using one out of three algorithms, overlap or DBSCAN.
print a help message
svdb --export --help
Export the variants of the database database.db:
svdb --export --db database.db
optional arguments:
--no_merge skip the merging of variants, print all variants in the db to a vcf file
--bnd_distance BND_DISTANCE the maximum distance between two similar precise breakpoints(default = 2500)
--overlap OVERLAP the overlap required to merge two events(0 means anything that touches will be merged, 1 means that two events must be identical to be merged), default = 0.8
--DBSCAN use dbscan to cluster the variants, overides the overlap based clustering algorithm
--epsilon EPSILON used together with --DBSCAN; sets the epsilon parameter(default = 500bp)
--min_pts MIN_PTS the min_pts parameter(default = 2
--prefix PREFIX the prefix of the output file, default = same as input
--memory load the database into memory: increases the memory requirements, but lowers the time consumption
Query
The query module is used to query one or more structural variant databases. Typically a database is constructed using the build module. However, since this module utilize the genotype field of the structural variant database vcf to compute the frequency of structural variants, a wide range of files could be used as database. The query module requires a query vcf, as well as a database file(either multisample vcf or SVDB sqlite database):
print a help message
svdb --query --help
Query a structural variant database, using a vcf file as query:
svdb --query --query_vcf patient1.vcf --db control_db.vcf
Query multiple databases, using a vcf file as query:
svdb --query --query_vcf patient1.vcf --db control_db1.vcf,control_db2.vcf --prefix test --in_occ default,Obs --in_frq FRQ,default --out_frq db1_AF,db2_Frq --out_occ db1_AC,db2_Obs
optional arguments:
-h, --help show this help message and exit
--db DB path to a db vcf, or a comma separated list of vcfs
--sqdb SQDB path to a SVDB sqlite db, or a comma separated list of dbs
--bedpedb BEDPEDB path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency, or a comma separated list of files
--in_occ IN_OCC The allele count tag, if used, this tag must be present in the INFO column of the input DB(usually set to AN or OCC). This parameter is required if multiple databases are queried.
--in_frq IN_FRQ The frequency count tag, if used, this tag must be present in the INFO column of the input DB(usually set to AF or FRQ). This parameter is required if multiple databases are queried.
--out_occ OUT_OCC the allele count tag, as annotated by SVDB variant(default=OCC). This parameter is required if multiple databases are queried.
--out_frq OUT_FRQ the tag used to describe the frequency of the variant(default=FRQ). This parameter is required if multiple databases are queried.
--prefix PREFIX the prefix of the output file, default = print to stdout. Required if multiple databases are queried.
--bnd_distance BND_DISTANCE the maximum distance between two similar breakpoints(default = 10000)
--overlap OVERLAP the overlap required to merge two events(0 means anything that touches will be merged, 1 means that two events must be identical to be merged), default = 0.6
--memory load the database into memory: increases the memory requirements, but lowers the time consumption(may only be used with sqdb)
--no_var count overlapping variants of different type as hits in the db
Merge
The merge module merges variants within one or more vcf files. This could be used to either merge the output of multiple callers, or to merge variants that are called multiple times due to noise or some other error:
print a help message:
python SVDB.py --merge --help
merge vcf files:
svdb --merge --vcf patient1_lumpy.vcf patient1_cnvnator.vcf patient1_TIDDIT.vcf > patient1_merged_callers.vcf
Similar variants will be merged, and presented according to the order of the input vcf files. I.e If lumpy and cnvnator calls the same variant in the top example,
the variant will be printed as the lumpy call. In most cases, the order should be set according to the accuracy or detail of the info field of the different callers.
The order could also be set using the --priority flag:
svdb --merge --vcf patient1_lumpy.vcf:one patient1_cnvnator.vcf:2 patient1_TIDDIT.vcf:tiddit --priority tiddit,2,one > patient1_merged_callers.vcf
In this example, tiddit will have the highest order, cnvnator second etc.
optional arguments:
-h, --help show this help message and exit
--bnd_distance BND_DISTANCE the maximum distance between two similar precise breakpoints
(default = 10000)
--overlap OVERLAP the overlap required to merge two events(0 means
anything that touches will be merged, 1 means that two
events must be identical to be merged), default = 0.6
--priority prioritise the input vcf files
--no_intra no merging of variants within the same vcf
--no_var variants of different type will be merged
--pass_only merge only variants labeled PASS
--same_order assume that the samples are ordered the same way (skip reordering and merging of the sample columns).