Filter/Intersect Manta SV's to target ROI (Region of interest) bed file

Illumina / manta

Structural variant and indel caller for mapped sequencing data

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Filter/Intersect Manta SV's to target ROI (Region of interest) bed file #195

Open gopi1616 opened 4 years ago

gopi1616 commented 4 years ago

Hello, is there way to filter the SV's called by manta with ROI in bed format. Bedtools intersect cannot be used for the complex SVs. Does Manta has any in-built tool for this or will there be one anytime soon? Thanks.

ctsa commented 4 years ago

A bed file of target regions can be specified, see:

https://github.com/Illumina/manta/tree/master/docs/userGuide#call-regions