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Hi,
I used deepsomatic(v.1.6.1) to call somatic mutations using ONT reads. But the process failed.
My parameter is --model_type=ONT_R104
**errors:**
```
2024-12-01 05:55:20.276827: I tensorflow/core/…
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I am attempting to run deepsomatic on the example data using the following command with a GPU node
```
export INPUT_DIR="${PWD}/test"
export OUTPUT_DIR="${PWD}/quickstart-output"
singularity exec \
…
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Hello there,
Thank you for creating and maintaining this amazing tool. The latest version of deepsomatic looks awesome!
I have been testing the latest docker image of deepsomatic (docker://google/de…
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Hi,
I used clairs(v0.4) to call somatic SNV/InDel(tumor/normal paired), but the PASS variants number is ~6w. Is it normal?
Compare to deepsomatic, the somatic SNV/InDel number is ~1.7w.
Do you …
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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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Hi, I attempted to run `deepsomatic` using Singularity. After converting the Docker image to a `.sif`, I used `--bind` to mount the input and output folders, but encountered the following error. Could…
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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,
I saw the HiFi somatic workflow https://github.com/PacificBiosciences/HiFi-somatic-WDL/blob/main/figures/simple_workflow_diagram.png. After calling somatic SNV/INDEL(using deepsomatic, tumor/no…
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Hi,
I saw the HiFi somatic workflow https://github.com/PacificBiosciences/HiFi-somatic-WDL/blob/main/figures/simple_workflow_diagram.png. After calling somatic SNV/INDEL(using deepsomatic, tumor/norm…
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Hi,
Thank you for providing this tool.
I noticed that you have updated to a new version (0.4.0). I would like to ask if it supports Indel calling for PacBio Revio.
Additionally, for HiFi data…