GASOLINE

GASOLINE is a collection of Perl, R and Fortran codes for the detection of germline and somatic SVs from long read sequencing data.

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patatoeking Edited 2023-07-17

Hi, I read your paper from biorx. I have not used the tool but I have some questions. Why does it take 3 hours for the tool to parse the Bam file? To detect somatic SVs couldn't you just use Sniffles2 or cuteSV(v2.0) to find the structural variants in a control sample, do the same thing with the cancer sample, and then compare the calls with the p-score like you did. I have used both Sniffles2 and cuteSV on about ~10x coverage ONT and they finish calling in like 5 minutes with 10cpu and 120G ram. I understand your clustering methods lead to better grouping and detection of small SVs. Is that the main focus of the tool? Why would I use this tool if it takes waayy longer than the competition with slightly better results? Are there any plans to improve the efficiency of the tool in the future? ALSO could you add in functionality where it does the somatic determination from 2 VCF files rather than having to both VCF files from scratch?

Reply from GASOLINE

Posted 2023-12-16

slightly better results? :)