gridsspostprocessvcf estimates Breakpoint INS like DEL.

lindenb / jvarkit

Java utilities for Bioinformatics

https://jvarkit.readthedocs.io/

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gridsspostprocessvcf estimates Breakpoint INS like DEL. #171

Closed gmgs-999 closed 3 years ago

gmgs-999 commented 3 years ago

Hi, I ran gridsspostporcessvcf and I saw a lot of DEL. I checked them in IGV and in vcf output of gridss, and all of them (I think) were INS of two breakends. Before running gridsspostprocessvcf(output of gridss) ins_example_1 After running it ins_example_2 In IGV ins_example_3

All INS marked as DEL I saw had svlen = 0. All single breakend INS (REF:A, ALT: .AAGG etc..) were well estimated. Is it a bug? Can I use the empirical rule that if an DEL has svlen=0 it's an insertion? Thanks!

lindenb commented 3 years ago

sorry, I'm afraid I don't support this tool : It's not even listed in http://lindenb.github.io/jvarkit/