# structural_variants.csv

Table of annotated structural variants provided by NYGC.
The SVs listed passed their high-confidence filtering, which included:
    Removing germline variants as listed in: DGV, 1000G, and an in-house
        blacklist
    One of:
        Called by more than one tool
        Called by only one tool but also confirmed by one or more of:
            A CNV changepoint (as found in copy_number_variants.csv)
            At least 3 split reads (in BE only).
            Any Crest-only calls (as these were found to be very specific)
Additionally, nearby SV events are merged if their breakpoints appear within
300 bps of each other (see methods)

# Columns:
DNANum {varchar} = DNANumber identifying unique samples to tie with other
    data tables
chr1/pos1/chr2/pos2 {integer} = the integer chromosome number and positions of
    the left/right breakpoint, respectively.
strand1/strand2 {varchar} = the strandedness of the breakpoint alignment.
SVtype {varchar[]} = the type of SV called by each of the callers that called
    this event.
CTX/DEL/DUP/INS/INV/ITX/TRA {integer} = the number of callers that called this
    event each of these SV types.
overlap {varchar[]} = A list of the callers that called the SV breakpoints that
    went into this event, in the same order as SVtype.
breakdancer/crest/delly {int} = the number of pre-merged pairs of SV
    breakpoints called by each of these callers that went into this SV event.
in_1000G/in_DGV/in_inHouse {bool} = True if this SV event is found in one of
    these databases of SVs (1000 Genomes Project call set, Database of
    Genomic Variants, or an in-house database of SVs called in germline
    genomes) (*** Maybe remove, since these are always false for this
    data set ***)
COSMIC {bool} = True if this is in the COSMIC database
gap {bool} = within centromere or telomere regions based on
    http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks20
Cancer_census {varchar[]} = list of Cancer Census genes affected by this SV
    event.
ClosestL/ClosestR {varchar} = gene closest to the SV (only for intergenic
    breakpoints) for the left/right breakpoint, respectively
Contained {varchar[]} = list of genes within the two SV breakpoints (but
    SV breakpoints are in intergenic regions)
DisruptL/DisruptR {varchar[]} = list of genes where the left/right breakpoint
    overlaps with the gene, and may potentially disrupt it.
Fusion {varchar} = list of genes fused as a result of this SV event.
Intronic {varchar} = list of genes which the SV event overlaps, but only
    affecting the intronic region.
closest_NBICseq_bkpt_to_pos1/2 {integer} = position of the closest copy number
    breakpoint as listed in copy_number_variants.csv.
tumor/normal_split_read_num_from_splazerS {integer} = the number of split
    reads, as reported by splazarS, in the BE or normal control sample,
    respectively
tumor/normal_1st/2nd_bkpt_pred_by_splazerS {integer} = the SV position for the
    first/ second breakpoint in the BE/ normal control sample, respectively.