Comments (3)
Hello, you could use e.g. mergevcf https://github.com/ljdursi/mergevcf to obtain a ShatterSeek compatible notation.
Best,
Isidro
from shatterseek.
Thanks, I understood that from the discussion in the issue section. but my second question was about the outputs from Manta, which are VCFs, so, what do I need to do we the SV-types from it and what is supported with ShatterSeek? I assume MergeVCF doesn't change anything from the VCF outputs from Manta, right? Do I need to use another tool for SV calls? if so, what would be your recommendation? Thanks
from shatterseek.
Hello, I would suggest that you try to use mergevcf as indicated above (please read the documentation) and/or convert the manta calls to the notation used in PCAWG (+/- for deletions; -/+ for duplications, etc). If you have questions about the output of manta it would be better for you to contact the developers of that tool. Hope this helps, Isidro
from shatterseek.
Related Issues (20)
- Link to visualizations is broken HOT 3
- Error in h (simpleError (msg, call)): Error when evaluating the argument 'x' in the method selection for function 'nrow': 'to' must be a finite number HOT 4
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- can't change color in plot_chromothripsis HOT 1
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- Warning when running sample data, error while plotting with chr no. and want to if shatter can be use with othrr organism data HOT 2
- plot_chromothripsis function is wrong HOT 1
- Error in statistical_criteria(): error in evaluating the argument 'x' in selecting a method for function 'nrow': wrong sign in 'by' argument HOT 2
- Only interchromosomal SVs used for chr_breakpoint_enrichment and pval_exp_chr ? HOT 4
- Error in statistical_criteria HOT 3
- Cannot allocate memory HOT 1
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