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 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:

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>

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.