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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, 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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#### Which new datasets are being added with this release?
#### What is the sample breakdown (number of WGS, WXS, RNA-Seq, Panel, Methylation, other)?
https://d3b.atlassian.net/browse/BIXU-3767
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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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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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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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Running the python version of this script using a .hap file with 42621 sites (snv file has 42621 lines), produces output haplotypes with 49028 sites! It's creating variant positions out of thin air!
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drdna updated
2 weeks ago
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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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SNV colors are updating as new SNVs are added, so the colors are changing since they're based on list indices
Maybe calculate a hash based on the SNV string, and then assign based on that?
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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 \…