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The README should include the source of a simple Biokepi pipeline (align FASTQs, call germline variants) and link to a tutorial which highlights the use of common bioinformatics tools.
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Hi,
I'm trying to use Pisces to call a tumour-only sample. I'm using the following command:
```shell
$ dotnet Pisces.dll -bam tumour.bam \
-CallMNVs false -g hs37d5 -gVCF false \
-i h…
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## Need
### TMB calculation today in BALSAMIC
The current definition is based on:
1. TMB was defined as the number of somatic, coding, base substitution, and indel mutations per megabase of genome …
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**Describe the bug**
Hello
From what I can see, Octopus in tumour-only calling mode sometimes does not detect heterozygous germline variants which have undergone loss of heterozygosity during tumo…
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e.g. B2M, TAP, &c.
Identifying loss in MHC might require running a custom program which first does genotyping of the germline MHC and then calls somatic variants against those specific alleles.
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Example:
```
self.conditional("combine_gatk_variants", [
(IsDefined(self.mutect2.out),
CombineVariants_0_0_8(
vcfs=[self.splitnormalisevcf.out, self.mutect2.out.assert…
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Funcotator is producing erroneous protein predictions for some variants.
A few include the following from `HG38` using `funcotator_dataSources.v1.6.20190124g.tar.gz`:
```
chr7 48227340 . CTTT…
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### Submitter Name
Kyle Moad/Rachel Karchin
### Submitter Affiliation
Johns Hopkins
### Submitter Github Handle
kmoad/RachelKarchin
### Additional Submitter Details
We are the PI and an enginee…
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### Submitter Name
Grace Pendlebury
### Submitter Affiliation
Shariant / Australian Genomics
### Submitter Github Handle
_No response_
### Additional Submitter Details
Shariant is…
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Hello, I seem to be having an issue with the germline module. I'm working on the bone marrow single cell sample provided in the GitHub. Upon running the germ line module, I can only detect a much smal…