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Combine structural variation outputs from long sequencing reads into a superior call set

combiSV 최신버젼 다운로드

최종 버전 다운로드 (.zip)

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# combiSV

Combine structural variation outputs from long sequencing reads into a superior call set

**Last updates: 22/04/22 version 2.3**  
- Includes now the REF and ALT sequences in the combined VCF               
**22/04/22**   
- combiSV now reports the END position and the allele depth calls (DR and DV), was needed to be compatible with SVanna              
**09/11/21**                                                                                                                         
- Only Sniffles, pbsv, SVIM or cuteSV are mandatory to run combiSV
- Improved precision

### Getting help

Any issues/requests/problems/comments that are not yet addressed on this page can be posted on [Github issues](https://github.com/ndierckx/Sim-it/issues) and I will try to reply the same day.

Or you can contact me directly through the following email address:

nicolasdierckxsens at hotmail dot com

### Cite

Dierckxsens, N., Li, T., Vermeesch, J.R. et al. A benchmark of structural variation detection by long reads through a realistic simulated model. Genome Biology, 22, 342 (2021). https://doi.org/10.1186/s13059-021-02551-4

### Prerequisites

Perl

### Instructions

Usage:

<code>perl combiSV2.1.pl -pbsv <pbsv_output.vcf> -sniffles <sniffles_output.vcf> -cutesv <cutesv_output.vcf> -nanovar <nanovar_output.vcf> -svim <svim_output.vcf> -nanosv <nanosv_output.vcf> -c <minimum_variance_allele_coverage> -o <output_name></code>

### Output

#### 1. output_name.vcf: 
This is the combined standard vcf output

#### 2. simplified_output_name.vcf: 
This is a simplified vcf output that can be used as input for Sim-it

#### 3. SVIM/Sniffles/pbsv/NanoVar/NanoSV_output_name.vcf: 
For each VCF input, an output file of the SVs that were retained is given.

combiSV

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