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Hello,
I encountered into some problems while using this native pav to call SV from assembly-hap and I tried many times and still couldn't make it. If you can give me some suggestions, I'd appreciat…
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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…
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Thanks for developing Strainy!
I'm trying to use amplicon-based Nanopore reads to figure out strain abundances in bacterial samples. The pool has 740 strains and each sample may contain ~10 of them. …
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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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### Need
As a geneticist I want to see true variants and not false positive calls. Currently we have databases for annotating variants that are commonly observed as somatic in highly filtered T+N c…
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The following command failed. Could you provide these files: snv_info/293T-snv_info.list1.bed and snv_info/293T-snv_info.list2.vcf ? Thanks!
python pmat-merge.py -i ${out_C_pmat} -f C -t T -r ${ref_g…
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Hello!
Previous version of ont-spectre (v0.2.1-alpha) stated that it can use SNV data to detect loss of heterozygosity (LoH) regions does it still apply to current (v0.2.2) version? If so, are there …
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Hello,
I have noticed that some of my outputs do not create a consensus or haplotype fasta file. I wanted to make sure I understood the issue so I looked at the `rvhaplo.sh` script and captured the…
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Hello,
For the gene-centric analyses, is there any possible way to obtain the number of SNVs per case and control samples? The output from the summary functions only lists the total number of SNVs …
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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