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Hi,
I'm using HMF tools for SV and CNV calling in tumor-normal matched and tumor-only mode and I've been running some test for samples for which I have the matched normal in both modes to compare the results. The problem appears when I'm running gripss (v2.3.4) since for some samples it calls much more SVs that in tumor-normal matched (it makes sense since there is no filtering of the germline variants), while for others it gives empty vcf so it hard-filters out all variants.
After some trials, I discovered that relaxation of the hard filter hard_max_normal_relative_support to 1 gives some results. Shouldn't these arguments be deactivated since there isn't the normal support?
I report here the code with parameters for both gridss and gripss:
Hi,
I'm using HMF tools for SV and CNV calling in tumor-normal matched and tumor-only mode and I've been running some test for samples for which I have the matched normal in both modes to compare the results. The problem appears when I'm running gripss (v2.3.4) since for some samples it calls much more SVs that in tumor-normal matched (it makes sense since there is no filtering of the germline variants), while for others it gives empty vcf so it hard-filters out all variants.
After some trials, I discovered that relaxation of the hard filter hard_max_normal_relative_support to 1 gives some results. Shouldn't these arguments be deactivated since there isn't the normal support?
I report here the code with parameters for both gridss and gripss:
gripss outcome when it filters all variants:
Are there suggested parameter values in tumor-only mode to have a comparable number of SVs?
Thank you in advance.
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