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cytham / nanovar

Structural variant caller for low-depth long-read sequencing data
GNU General Public License v3.0
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How to use nanovar to do population-scale SV calling? #8

Closed xiekunwhy closed 4 years ago

xiekunwhy commented 4 years ago

Hi,

How to use nanovar to do population-scale SV calling when there a lot of samples (like Iceland populaiton https://www.biorxiv.org/content/10.1101/848366v1)?

Best wishes Kun

cytham commented 4 years ago

Hi Kun,

NanoVar is a genomic SV caller. It detects SVs from long-read WGS data. For SV analysis on a population-scale, NanoVar is only involved in SV discovery where it detects SVs for individuals in the population, generating a VCF file for each individual. Any downstream analysis from the VCF files requires other tools and databases. I am currently developing a SV analysis tool which can annotate and compare SVs in a cohort. Hopefully it will be ready in the next month.

As for now, you can probably begin by aggregating the SVs from all the individual VCF files and discover hotspot clusters of SVs shared among most individuals.

Best, cy

xiekunwhy commented 4 years ago

Hi cy,

Thank you for your reply, hope tools coming soon.

Best, Kun