mkirsche
commented
2 years ago Hi,
Thanks for your interest in using Jasmine! In order to use min_overlap alone, I would recommend setting "max_dist_linear=1.0". This will ensure that any two variants which have at least 50% reciprocal overlap will also satisfy the maximum breakpoint distance threshold, essentially removing the threshold from consideration.
I hope that helps! Melanie
jasmine can merge SVs across samples and tools.
i want to merge SVs detected for different samples and different tools, and two overlapping CNVs with RO > 50% were treated as the same region. so i write this command. jasmine file_list=/bak01/filelist.txt out_file=/bak01/merge_metasv_delly/merge.vcf --min_overlap 0.5 --output_genotypes --default_zero_genotype --leave_breakpoints I wonder if --min-overlap can be used alone. because you reply in this question, when using min_overlap, Jasmine still take "max_dist_linear" or "max_dist" into account to decide to merge. https://github.com/mkirsche/Jasmine/issues/13. thank you !