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It would be nice to add a process to compute MSIs for tumor-only samples:
https://github.com/niu-lab/msisensor2
I could take care of this.
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@MareikeJaniak can u share the debug logs for these 7 protocols for the new dnaseq (tumor pair merged) in 5.0?
'germline_snv', 'germline_sv', 'germline_high_cov', 'somatic_tumor_only', 'somatic_fas…
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Thanks you for your excellent works, I want to know whether this work is a equal way to augment data.
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Hi!
I would like to know if it is possible to use Smurf with tumor-only mode.
I know VarScan and Strelka2 can`t work with tumor-only, so I would have only the VCFs for freebayes, GATK and VarDict. I…
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Add 7316-1106 and 7316-3000 back to hope subcohort, except for proteomics. Use the attached file from Pei.
[master_11032023 (1).txt](https://github.com/user-attachments/files/15892642/master_11032023…
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I have nanopore long-reads from tumor (tumor only)
I also have SNP/indel variant calls from the same sample from illumina in both germline (normal) and tumor data
I want to try and phase the tumou…
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Hi,
Thank you for your improvment for tumor-only analysis. Could you give us more informations about the method used please ?
Bests,
Elodie
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Hello ,
I read given Documents and provide good document details for understanding logic parts.
i have some different type of label Like
1) only cover Color
2) only cover Size/Shape
3) onl…
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Hi everyone,
Can I use this workflow for tumor only variant calling to detect both Somatic and Germline variants? Or should I first run my data with Mutect in tumor only mode and then use varlocira…
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Hello.
I read you recommend at least 20 samples to make the baseline. However I don´t have that many.
Can you send me the baselines file are for GRCh38 that you mention in another posts?
Thx