
COMMAND LINE USAGE

       $ANNOTSV/bin/AnnotSV -SVinputFile 'Path of your VCF or BED input file with SV coordinates' >& AnnotSV.log &


OPTIONS

-annotationsDir:                Path of the annotations directory

-annotationMode:                Description of the types of lines produced by AnnotSV
                                Values: both (default), full or split

-bcftools:                      Path of the bcftools local installation

-bedtools:                      Path of the bedtools local installation

-benignAF:                      Allele frequency threshold to select the benign SV in the data sources
                                Range values: [0.001-0.1], default = 0.01 (i.e. 1%)	

-candidateGenesFile:            Path of a file containing the candidate genes of the user (gene names can be space-separated, tabulation-separated, or line-break-separated)

-candidateGenesFiltering:       To select only the SV annotations ("split" and "full") overlapping a gene from the "candidateGenesFile"
                                Values: 0 (default) or 1

-candidateSnvIndelFiles:        Path of the filtered VCF input file(s) with SNV/indel coordinates for compound heterozygotes report (optional)
                                Gzipped VCF files are supported as well as regular expression

-candidateSnvIndelSamples:      To specifiy the sample names from the VCF files defined from the -candidateSnvIndelFiles option
                                Default: use all samples from the filtered VCF files

-genomeBuild:                   Genome build used
                                Values: GRCh38 (default) or GRCh37 or mm9 or mm10

-help:                          More information on the arguments

-hpo:                           HPO terms list describing the phenotype of the individual being investigated
                                Values: use comma, semicolon or space separated class values
                                Default = "" (e.g.: "HP:0001156,HP:0001363,HP:0011304")

-includeCI:                     To expand the "start" and "end" SV positions with the VCF confidence intervals (CIPOS, CIEND) around the breakpoints
                                Values: 1 (default) or 0

-metrics:                       Changing numerical values from frequencies to us or fr metrics (e.g. 0.2 or 0,2)
                                Values: us (default) or fr

-minTotalNumber:                Minimum number of individuals tested to consider a benign SV for the ranking
                                Range values: [100-1000], default = 500

-outputDir:                     Output path name

-outputFile:                    Output path and file name 

-overlap:                       Minimum overlap (%) between user features (User BED) and the annotated SV to be reported
                                Range values: [0-100], default = 100

-overwrite:                     To overwrite existing output results
                                Values: 1 (default) or 0

-promoterSize:                  Number of bases upstream from the transcription start site
                                Default = 500

-rankFiltering:                 To select the SV of a user-defined specific class (from 1 to 5)
                                Values: use comma separated class values, or use a dash to denote a range of values
                                (e.g.: "3,4,5" or "3-5"), default = "1-5"

-reciprocal:                    Use of a reciprocal overlap between SV and user features (only for annotations with features overlapping the SV)
                                Values: 0 (default) or 1

-REreport:                     Create a report to link the annotated SV and the overlapped regulatory elements (coordinates and sources)
                                Values: 0 (default) or 1

-REselect1:                     To report only the morbid, HI, TS, candidate and phenotype matched genes 
                                Values: 1 (default) or 0
	
-REselect2:                     To report only the genes not present in "Gene_name"
                                Values: 1 (default) or 0

-samplesidBEDcol:               Number of the column reporting the samples ID for which the SV was called (if the input SV file is a BED)
                               	Range values: [4-[, default = -1 (value not given)
                                (Samples ID should be comma or space separated) 

-snvIndelFiles:	                Path of the VCF input file(s) with SNV/indel coordinates used for false positive discovery
                                Use counts of the homozygous and heterozygous variants
                                Gzipped VCF files are supported as well as regular expression

-snvIndelPASS:                  Boolean. To only use variants from VCF input files that passed all filters during the calling (FILTER column value equal to PASS)
                                Values: 0 (default) or 1

-snvIndelSamples:               To specify the sample names from the VCF files defined from the -snvIndelFiles option
                                Default: use all samples from the VCF files

-SVinputFile:                   Path of the input file (VCF or BED) with SV coordinates
                                Gzipped VCF file is supported

-SVinputInfo:                   To extract the additional SV input fields and insert the data in the outputfile
                                Values: 1 (default) or 0

-SVminSize:                     SV minimum size (in bp)
                                AnnotSV does not annotate small deletion, insertion and duplication from a VCF input file 
                                Default = 50

-svtBEDcol:                     Number of the column describing the SV type (DEL, DUP) if the input SV file is a BED
                                Range values: [4-[, default = -1 (value not given)

-tx:                            Origin of the transcripts (RefSeq or ENSEMBL)
                                Values: RefSeq (default) or ENSEMBL

-txFile:                        Path of a file containing a list of preferred genes transcripts to be used in priority during the annotation (Preferred genes transcripts names should be tab or space separated)

-variantconvertDir:             Path of the variantconvert directory
				(by default, the variantconvert tool distributed by annotSV is used)

-vcf: 				Creation of a VCF output file format (-svtBEDcol needs to be defined too)
				Values: 0 (default) or 1


