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bioinform / metasv

MetaSV: An accurate and integrative structural-variant caller for next generation sequencing
http://bioinform.github.io/metasv/
BSD 2-Clause "Simplified" License
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how to merge overlapping svs #75

Open crazyhottommy opened 9 years ago

crazyhottommy commented 9 years ago

Hi there,

Reading the metaSV paper. I am interested in how do you implement the "Merge overlapping calls per tool (intra-tool merging)"

I have read a post on bedtools google group https://groups.google.com/forum/#!topic/bedtools-discuss/JXZbJSwVxUo

where can I get the script for merging overlapping vcf files?

Thanks! Ming

marghoob commented 8 years ago

Hi Ming

Apologies for the late reply due to a combination of travels and other deadlines. The merging of overlapping calls from multiple files is implemented internally in MetaSV. You can have a look at the merge_intervals and merge_intervals_recursively functions in https://github.com/bioinform/metasv/blob/master/metasv/sv_interval.py to get a better idea.

Best Marghoob.