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Hi team
Command used:
`spectre CNVCaller --coverage mosdepth/"$A".regions.bed.gz --sample-id $A --output-dir spectre2 --reference ~/beggsa-clinicalnanopore/genomes/grch38/genome.fa --metadata …
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Hi,
So I recently pulled the Singularity image of PAV `2.4.2.1` which I have used in parallel on a "large" number of assemblies. All the jobs eventually failed after some time so I restarted it on …
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Thank you for the great pipeline! Following your intrinsic instructions, I have successfully run through the fantastic pipeline for Somatic SNV calling from scRNA-seq. However, I found that the cellS…
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Hi, thanks for developing this tool
I run the script of vcf2phylip.py successfully but found the output seems to be the amino acid sequences. My code and the screenshort of my output file are as fo…
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I am calling CNVs in tumour ONT long-reads and want to try using spectre
I assume it is preferred to input SNPs from a matched tumour sample rather than germline SNPs? Or would germline SNPs be mor…
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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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**Describe the bug**
Unable to upload images for the report when calling `ipr_report`.
**To Reproduce**
Steps to reproduce the behavior:
1. Run command `ipr_report`
2. with input:
```
{
…
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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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This feature involves switching our tiering for the filtered events table (currently based on the CGC dataset) to the more informative OncoKB API.
**Responsibilities:**
- **Column Set Definition…
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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, …