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mcmero / SVclone

A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.
BSD 3-Clause "New" or "Revised" License
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SVclone annotate skipping SV events #22

Closed kbredemeyer closed 3 years ago

kbredemeyer commented 3 years ago

Hi Marek, I've been having some trouble getting SVclone to run on some Manta vcfs and keep getting a string of the following errors.

Initially: SV MantaBND:4:163646:163651:0:1:0:1 improperly paired or missing attributes

And later in the run: Warning: record GWNJ-1012:554:GW2106121243rd:4:2161:9390:8015 contains invalid attributes, skipping

This is after manually changing bam associated parameters in the config.ini file as other issues have suggested. I still get an output in simplified format where reciprocal translocations are merged, but all DEL and DUPs are missing. Maybe I just missed something in the documentation? Wondering what might be causing these skipped SVs. Thanks, Kevin

mcmero commented 3 years ago

We haven't tested SVclone with Manta's SVs. Looking at the VCF output format, the deletion/duplication format is incompatible with SVclone's interpretation. I can look into adding this in the future, but for the moment you may have to make a script to process Manta's VCF data into SVclone's simple SV input format.

kbredemeyer commented 3 years ago

Ok I'll see what I can figure out. Thank you for your quick response! -K

mcmero commented 3 years ago

I'll just add that if you find a workable solution, please feel free to submit a pull request. For reference, this is the code that handles the SV processing from VCF I imagine support for those manta single-record SVs could be added by using the "END" INFO field instead of pairing the mate SV record.