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I've been trying to replicate the runtime of a WES sample using the same BAMs as the ones specified in https://raw.githubusercontent.com/google/deepvariant/r1.6/scripts/inference_deepvariant.sh
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https://www.ncbi.nlm.nih.gov/pubmed/30297909
- [ ] [create a issue on datahub](https://github.com/cBioPortal/datahub/issues/new) before curating a study (one issue per study) and copy this checklis…
jjgao updated
8 months ago
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## Need
It would be good to start tracking GC and AT dropout for all WGS cases. Right now we are just doing it for panels.
## Suggested approach
Run picard hs metrics also on WGS cases. Preferabl…
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### What you did:
I searched for a specific variant from the search bar (22-20037009-TG-T) in gnomAD v4 after finding it first in gnomAD v2.1.1 (22-20024532-TG-T).
I was viewing the variant …
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The issue is literally as described in the title: `export_probabilities_per_mutation=True` leads to an error with `exome=True`. However, it works when `exome=False`.
An example run is as follows:
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From the [docs](https://glow.readthedocs.io/en/latest/etl/variant-data.html#vcf):
> For the sharded VCF writer, the sample IDs are inferred from the first row of each partition and must be the same f…
Hoeze updated
6 months ago
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Dear Team
I ran the following pipeline to estimate the CCF of the variants reported in a mutect 2.1 VCF.
The pipeline goes well but in the "sorted_variants.csv" output are printed out only 30000 va…
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Hi,
I am running:
from SigProfilerMatrixGenerator import install as genInstall
genInstall.install('GRCh38', rsync=False, bash=True)
from SigProfilerSimulator import SigProfilerSimulator as sigS…
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### What I did:
Comparing this:
https://gnomad.broadinstitute.org/variant/1-161518015-T-C?dataset=gnomad_r4
to the v4 exome and genome VCFs downloaded from gnomAD website, I've observed a d…
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### Description of the bug
I am getting a new type of error when running the same sample samplesheet as it used to work before:
```
The sample-sheet only contains tumor-samples, but the following…