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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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Output ".seg" file [Feature Request] #3

Open ahwanpandey opened 5 years ago

ahwanpandey commented 5 years ago

It would be great if the tool would output a ".seg" file that you can load into IGV. It's easy enough to parse the VCF but just some that that would be nice to have out of the box. If you agree, having a "--sample-id" parameter to use for the name in the ID column would be very convenient as well.

https://software.broadinstitute.org/software/igv/SEG

dariober commented 5 years ago

Thanks - I'll keep this in mind but for now I may leave it to the user to prepare the desired file for IGV.

natalie-23-gill commented 2 years ago

The format_igv_seg function in facets-suite might be an easy way to incorporate this