Discovering AnnotSV? test.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 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.
-genomeBuild:
GRCh38
GRCh37
mm9
mm10
Genome build
-samplesidBEDcol:
Number of the column reporting the samples ID for which the SV was called
-hpo (optional):
HPO terms list describing the phenotype of the individual being investigated
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
-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"
-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
-minTotalNumber: Minimum number of individuals tested to consider a benign SV for the ranking
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
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
Annotation and ranking of your SV are freely available online. Please, fill the form below and submit.
Results are powered for visualization by knotAnnotSV.
An interactive circos plot generated by vcf2circos is also available.