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‎README.md

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#modules:
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SVDB consists of five separate modules that are used to manage, query and create structural variant databases. These are the modules:
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Build:
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This module is used to construct structural variant databases from vcf files. It is activated using the folowing command:
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python svdb.py --build
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for more information type:
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python SVDB.py --build --help
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Hist:
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This module is used to compare structural variant vcf files, either by generating a similarity matrix, or by creating histograms of the efficency of databases of different sizes(based on input vcf files). The module is activated through this command:
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python svdb.py --hist
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for more information type:
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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. These are the commands used to construct a structural variation database:
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print a help message
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python SVDB.py --build --help
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Construct a database, from a set of vcf files:
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python SVDB.py --build --vcf sample1.vcf sample2.vcf sample3.vcf
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construct a database from vcf files stored in a folder
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python SVDB.py --build --folder SV_analysis_folder/
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optional arguments:
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-h, --help show this help message and exit
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--no_merge skip the clustering of variants
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--ci overides overlap and bnd_distance,determine hits based
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on the confidence interval of the position fo the
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variants(0 if no CIPOS or CIEND is vailable)
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--bnd_distance BND_DISTANCE the maximum distance between two similar precise
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breakpoints(default = 2500)
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--overlap OVERLAP the overlap required to merge two events(0 means
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anything that touches will be merged, 1 means that two
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events must be identical to be merged), default = 0.8
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--files [FILES [FILES ...]] create a db using the specified vcf files(cannot be
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used with --folder)
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--folder FOLDER create a db using all the vcf files in the folders
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--prefix PREFIX the prefix of the output file, default = SVDB
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Hist: This module is used to compare structural variant vcf files, either by generating a similarity matrix, or by creating histograms of the efficency of databases of different sizes(based on input vcf files):
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print a help message
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python SVDB.py --hist --help
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Query:
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The query module is used to query a structural variant database. Typically a database is constructed using the build module. However, since this module utilize the genotype field of the sructural 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 vcf.
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python SVDB.py --query
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for more info, type
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Create histograms of different sizes, and compute their efficiency:
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python --hist --sample_hist -folder input
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Create a similarity matrix of the selected sampes:
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python --hist --similarity_matrix -folder input
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optional arguments:
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-h, --help show this help message and exit
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--files [FILES [FILES ...]] input vcf files(cannot be used with folder)
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--k [K [K ...]] the sizes of the sampled databases
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default = n=10*i < samples(used with sample_hist)
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--n N the number of iterations,default=100(used with sample_hist)
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--bnd_distance BND_DISTANCE the maximum distance between two similar precise
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breakpoints(default = 10000)
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--overlap OVERLAP the overlap required to merge two events(0 means
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anything that touches will be merged, 1 means that two
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events must be identical to be merged), default = 0.6
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--ci overides overlap and bnd_distance,determine hits based
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on the confidence interval of the position of the
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variants(0 if no CIPOS or CIEND is vailable)
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Query: The query module is used to query a structural variant database. Typically a database is constructed using the build module. However, since this module utilize the genotype field of the sructural 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 vcf:
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print a help message
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python SVDB.py --query --help
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Purge:
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The purge module is used to remove entries from a database. These entries could be sensitive information such as disease causing variants. THe purge module is run using this command:
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python SVDB.py --purge
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for more info, type
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Query a structural variant database, using a vcf file as query:
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python SVDB.py --query --query_vcf patient1.vcf --db control_db.vcf
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optional arguments:
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-h, --help show this help message and exit
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--hit_tag HIT_TAG the tag used to describe the number of hits within the
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info field of the output vcf(default=OCC)
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--frequency_tag FREQUENCY_TAG the tag used to describe the frequency of the
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variant(defualt=FRQ)
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--prefix PREFIX the prefix of the output file, default = print to stdout
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--bnd_distance BND_DISTANCE the maximum distance between two similar precise breakpoints
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(default = 10000)
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--overlap OVERLAP the overlap required to merge two events(0 means
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anything that touches will be merged, 1 means that two
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events must be identical to be merged), default = 0.6
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--no_var count overlaping variants of different type as hits
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--invert invert the sorting order so that high frequency
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samples are present on top of the output vcf
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--ci overides overlap and bnd_distance,determine hits based
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on the confidence interval of the position fo the
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variants(0 if no CIPOS or CIEND is vailable)
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Purge: The purge module is used to remove entries from a database:
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print a help message:
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python SVDB.py --purge --help
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Merge:
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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.
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python SVDB.py --merge
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for more info, type
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Delete a sample from a DB, the sample id should be the same as the id written in the format columns of the db:
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python SVDB.py --purge --sample patient2 --db my_svdb.vcf > cleaned_db.vcf
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Delete variants from a DB, the variants should be stored in a standard structural variant format:
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python SVDB.py --purge --vcf delete_these_variants.vcf --db my_svdb.vcf > cleaned_db.vcf
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optional arguments:
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-h, --help show this help message and exit
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--bnd_distance BND_DISTANCE the maximum distance between two similar precise breakpoints
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(default = 10000)
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--overlap OVERLAP the overlap required to merge two events(0 means
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anything that touches will be merged, 1 means that two
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events must be identical to be merged), default = 0.6
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--ci overides overlap and bnd_distance,determine hits based
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on the confidence interval of the position fo the
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variants(0 if no CIPOS or CIEND is vailable)
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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:
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print a help message:
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python SVDB.py --merge --help
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merge vcf files:
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python SVDB.py --merge --vcf patient1_lumpy.vcf patient1_cnvnator.vcf patient1_TIDDIT.vcf > patient1_merged_callers.vcf
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optional arguments:
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-h, --help show this help message and exit
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--bnd_distance BND_DISTANCE the maximum distance between two similar precise breakpoints
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(default = 10000)
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--overlap OVERLAP the overlap required to merge two events(0 means
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anything that touches will be merged, 1 means that two
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events must be identical to be merged), default = 0.6
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--ci overides overlap and bnd_distance,determine hits based
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on the confidence interval of the position fo the
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variants(0 if no CIPOS or CIEND is vailable)
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--no_intra no merging of variants within the same vcf
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--no_var variants of different type will be merged
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--pass_only merge only variants labeled PASS

‎SVDB.py

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parser.add_argument('--overlap', type=float, default = 0.95,help="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 = 0.95")
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parser.add_argument('--ci', help="overides overlap and bnd_distance,merge based on the confidence interval of the position fo the variants(0 if no CIPOS or CIEND is vailable)", required=False, action="store_true")
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parser.add_argument('--no_intra', help="no merging of variants within the same vcf", required=False, action="store_true")
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parser.add_argument('--no_var', help="variants of different type will be merged", required=False, action="store_true")
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parser.add_argument('--pass_only', help="merge only variants labeled PASS", required=False, action="store_true")
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args= parser.parse_args()
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SVDB_merge_vcf_module.main(args)
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else:

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