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It would be great to compare DeepSomatic & ClairS output or to generate a consensus vcf using both
https://github.com/google/deepsomatic
https://github.com/google/deepsomatic/blob/r1.6.1/docs/deep…
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Hi,
I installed deepsomatic 1.7.0(python 3.10.12), but run failed. The log is below:
2024-09-25 13:03:51.979669: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is op…
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DeepSomatic was recently released as an extension of DeepVariant that enables tumor-normal somatic calling. I would like to try adding this to Sarek.
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I am currently looking to call very small minor variants (e.g. less than 1%) using super deep HiFi data with ~8000 coverage for pseudomonas aeruginosa, is deep variant appropriate to use in this case?…
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Release tar and zip files do not contain any source. Is it possible to run this without docker? This is hinted at in the readme but it seems like there is a missing section or two.
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I ran Deepsomatic's WGS_TUMOR_ONLY model using singularity (version: v17_rc1_08082024). I used the run_deepsomatic command but the process was interrupted after 24 hours. Can DeepSomatic resume the jo…
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Issue by @MaxUlysse, moved from SciLifeLab#666
- [ ] [ExpansionHunter](https://github.com/Illumina/ExpansionHunter) for estimating repeat sizes
- [ ] [QDNAseq](https://github.com/ccagc/QDNAseq) CN…
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Hi,
is ti possible to run deepsomatic on matched tumor-normal rnaseq samples ?
from a previous issue, it seems that the WES mode is the way to run this case. Is this tested ?
In deepvariant the …
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Hello,
Thank you for developing those fancy variant callers.
We conducted short-read RNA sequencing, and since we do not have a control sample, we are planning to call variants using the DeepSom…
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Matched tumor-normal analyses can be problematic if the normal sample has issues, is missing for any reason, or simply has an outlier genotype. A better approach, currently as far as I know only impl…