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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 get phasing inf…
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Hi,
I am wondering how the tumor only functionality differs in these two versions of the MSIsensor software, and if one should be selected in preference over the other?
Thanks in advance!
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In order to classify Kits 23 and Tumor subtype, can tumor classification be made using only segmntation.nii.gz files based on the "tumor_histologic_subtype": "xxxx", key and value from the json file? …
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Is there a set of instructions that we should follow for running this in tumor-only mode? For example, what should we put for the NormalMetrics field in the config file?
vymao updated
4 years ago
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**Describe the issue**
I am using the funciton `tcgaCompare`. Depending on the whether I plot each of my cohorts individually or add them all to one tcgaCompare plot, the results change.
**Com…
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Hi,
I tried to use the markdown published on https://ropensci.org/blog/2019/09/06/ucscxenatools-surv/
This is what happens:
merged_data = tibble(sampleID = names(KRAS),
…
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Hi,
We have 91 cram files that we need to run through the tumor-only pipeline. Should we run the baseline step with all the 91 files or randomly take a subset? Please let me know.
Thanks!
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I would have a proposal for a TMB calculation module. It assumes tumor-only sequencing and requires only a VCF and BED file as input and works following this procedure:
- The annotated VCF will be …
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### Description of the bug
As you mention in your Nextflow pipeline: @https://nf-co.re/sarek/3.0.2/parameters it would be possible to obtain the results of tumor-only somatic variant calling using st…
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### Description of the bug
Hi,
I ran the pipeline (`3.1.2`) for a bunch of tumor-only WGS samples. CNVkit reference bed files have both target and antitarget with improper bin counts:
```
wc -l *.…