satellite_altPhenoSV

Model

PhenoSV PhenoSV-light choose from PhenoSV (default mode with 238 features) and PhenoSV-light (lighter and faster version with only 42 features, works well on most of SV types except translocations)

Genome

GRCh38 GRCh37

Chromosome

chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY

SV Type

deletion duplication insertion inversion

Start

Start position of SV.

End

End position of SV.

assignmentUpload SV files to PhenoSV

csv and bed files are supported to score deletions, duplications, inversions, and insertions (<10 SVs). bedpe files are supported to score translocations (<5 SVs). Input file examples can be found here. Note that, we don't generate PhenoSV scores for SVs (coding and noncoding) affecting more than 10 genes. Please use the command line tool for full results.

5' Chromosome

chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22

5' Breakpoint

5' Breakpoint position.

5' Strand

+ -

3' Chromosome

chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22

3' Breakpoint

3' Breakpoint position.

3' Strand

+ -

Human Phenotype Ontology (HPO) Term ID List

Please enter HPO term IDs if available, otherwise leave it blank. The entries will be ignored if uploaded file contains HPO information. HPO terms should in the format of HP:digits, e.g., HP:0000707, separated by semicolons, newlines, commas, or spaces.

α

Scaling parameter controlling for the degree of using phenotype-genotype associations to refine PhenoSV scores. Please enter a positive value, with larger values representing higher impacts of phenotype information on PhenoSV and 0 represents no impacts.

Inference Mode

default mode - infer direct impacts of coding SVs and indrect effects of noncoding SVs full mode - infer both direct and indirect impacts of coding SVs and indirect effects of noncoding SVs

Inference Scope

distance - infer SV indirect effects on genes within 1Mbp of upstream and downstream tad - infer SV indirect effects on genes based on TAD annotations

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