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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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Specifying specific regions to INCLUDE when variant calling (done adaptive sampling for nanopore sequencing) #72

Closed nbertholdpgc closed 1 month ago

nbertholdpgc commented 11 months ago

Hi all. I have a question about the filtering process for targeting particular regions. I know you can supply a bed file to specify regions to EXCLUDE from variant calling. However, I have performed adaptive sampling for my nanopore sequencing and have 8 regions of 200kb in size. I suppose I could supply a bed file for the exclusion flag with everything except my 8 target regions, but I'm wondering if theres a more efficient way?

Cheers guys!!

cytham commented 10 months ago

Hi @nbertholdpgc, sorry for the late reply. NanoVar has not been tested to work with adaptive sampling data from nanopore sequencing and there might be some issues with overall coverage. However, you can still give it a try and let me know how it goes. Regarding the target regions, I suggest to just run NanoVar without any filters, and then doing some filtering on the VCF output if you require, maybe using bcftools. The filtering option in NanoVar is mainly to exclude low-complexity regions to reduce false positives.

cytham commented 1 month ago

Closed due to inactivity