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Hello,
I think Susie can only handle multi-allelic variants when these have been split into biallelic variants - is this correct? Unfortunately this isn't always easy to do (especially for CNV whe…
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Hi!
I'm attempting to use ont-spectre for CNV calling on our data by using the following command:
```
spectre CNVCaller \
--bin-size 1000 \
--coverage $MOSDEPTH \
--sample-id $SAMPLE \…
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When I use the instrain compare -bams parameter, I consistently encounter the following issue:‘’
“ValueError: error during iteration
BlockingIOError: [Errno 11] Resource temporarily unavailable
Exc…
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### Need
As a pipeline user, I want to better balance the input to DeepVariant, to allow for faster and more parallelised processing of samples. Currently, regions are input as whole to DeepVariant, …
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To be calculated by production team and added to Stats page after
Related: https://github.com/broadinstitute/gnomad_production/issues/1438
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Hi Team,
I tried this package using the same input as with signature.tools.lib. The SNV catalogue is generated from tabToSNVcatalogue, and the ID catalogue is generated by SigProfilerMatrixGenerato…
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### Description of the bug
ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (
earlycasualcaiman)' …
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Hi,
I have been running preprocess step and then germline snv calling on my Mac. However, all my outputs in .gl.vcf.gz have zero bytes. Are there any errors? Would the problem be the different v…
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### Description of feature
DeepTrio has had an update where it improved a lot from previous versions. Could consider adding it.
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First attempt since my last round of queries... running with Clair3 SNVs and get:
```
Traceback (most recent call last):
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre…