Discovering AnnotSV?
- Download a SV input file example (VCF): test.vcf
- Or ask for an automatic loading of this SV input file example (VCF):
no
yes
- Or enter the coordinates of your SV of interest followed by its SV type:
Submit
A job ID will be provided at the time of data submission. It allows you to bookmark and access the results at a later time.
Moreover, the status of the job (running or finished) will be reported.
SV input file options
-SVinputFile:
SV Input file: VCF (.vcf/.vcf.gz) or BED (.bed) format . Please respect the extension file.
VCF file should be compliant with the VCF v4.3 . BEDPE are not accepted .
-SVinputInfo:
0
1
To extract the additional SV input fields and insert the data in the output file
-svtBEDcol:
The column number describing the SV type (DEL, DUP...) if the input SV file is a BED.
4th column = 4
Range values: 4 or more, default = -1 (value not given)
-genomeBuild:
GRCh38
GRCh37
mm9
mm10
Genome build
-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 = 5 (Samples ID should be comma or space separated)
Phenotype-driven analysis (extracted from Exomiser) options
-hpo (optional):
HPO terms list describing the phenotype of the individual being investigated
Values: use comma, semicolon or space separated class values
(e.g.: "HP:0001156,HP:0001363,HP:0011304")
General options
-metrics:
us
fr
Changing numerical values metrics: us (0.2) or fr (0,2)
-promoterSize:
500
1500
2500
3500
Number of bases upstream from the transcription start site
-SVminSize:
SV minimum size (in bp)
-annotationMode:
both
full
split
Description of the types of lines produced by AnnotSV
-rankFiltering:
To select the SV of a specific class : from 1 (benign) to 5 (pathogenic); or NA
Values: use comma separated class values, or use a dash to denote a range of values, default = "1-5,NA"
( e.g.: "3,4,5" or "3-5")
-includeCI:
1
0
To expand the "start" and "end" SV positions with the VCF confidence intervals (CIPOS, CIEND) around the breakpoints
Genes options
-candidateGenesFile (optional):
File containing your candidate genes (gene names can be space-separated, tabulation-separated, or line-break-separated). Only used for the ranking.
-candidateGenesFiltering:
0
1
To select only the SV "split" annotations overlapping a gene from the "candidateGenesFile"
Transcripts options
-tx:
RefSeq
ENSEMBL
Origin of the transcripts (NCBI or ENSEMBL)
-txFile (optional):
To specify a list of preferred genes transcripts to be used during the annotation (optional)
Benign SV setting options
-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%)
-minTotalNumber:
Minimum number of individuals tested to consider a benign SV for the ranking
Range values: [100-1000]
Regulatory element options
-REselect1:
1
0
To report only the morbid, HI, TS, candidate and phenotype matched genes
-REselect2:
1
0
To report only the genes not present in "Gene_name"
False positive deletion discovery options
-snvIndelFiles (optional):
VCF (.vcf/.vcf.gz) input file with SNV/indel coordinates used for false positive discovery
-snvIndelPASS:
0
1
To only use variants from snvIndelFiles that passed all filters during the calling (FILTER column value equal to PASS)
-snvIndelSamples (optional):
To specify the sample names from the VCF files defined from the -snvIndelFiles option
Default: use all samples from the VCF files
Compound heterozygosity analysis options
-candidateSnvIndelFiles (optional):
Filtered VCF (.vcf/.vcf.gz) input file with SNV/indel coordinates used for compound heterozygotes report
-candidateSnvIndelSamples (optional):
To specifiy the sample names from the VCF files defined from the -candidateSnvIndelFiles option
Default: use all samples from the filtered VCF files