-
Dear Author,
Firstly, I would like to express my gratitude for developing this valuable tool for researching recent pathogen transmission. Your work has significantly contributed to the field.
I hav…
-
With release 156, now dbSNP includes rsIDs larger than 2^31 which cannot be properly handled by `bcftools` anymore:
```
$ wget https://ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.…
-
Hi
Thank you for creating this tool. I've been trying to use this with some nanopore gridion data. It keeps getting stuck on the following lines
haplodmf.sh: line 497: 57 Killed …
-
### Description of the bug
Aug-12 14:30:26.359 [TaskFinalizer-10] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEP…
-
Hello,
This site is my go-to resource for identifying lineages based on mutations in wastewater, and I've been sharing it with colleagues who really appreciate it, too. I am now looking specifical…
-
Hi,
for SNVs, one can easily calculate confidence intervals for the dN/dS ratios per gene using the `geneci()`, which is really useful. However, it only calculates confidence intervals for SNV classe…
-
Hi guys!
I have some suggestions for improvement of the "Search SNVs and Indels" function which is actually a very useful tool to check mutation burden in a cohort compared to control cohorts.
h…
-
Hi,
This issue is a suggestion more than a problem. Adding an option to call exclusively SVs (and maybe also exclusively SNVs or INDELs) would be useful to save time. For example, I'm only interes…
-
Hi. @luisgls @hanasusak
I want to estimate CCF using the CCF function but I found it required a input of CCF_CNV, which is defined as:
`cancer cell fraction of somatic SNV in region with reported S…
-
Hi,
I want to co-phase SNVs and STRs.
I've placed the str VCF file as the --sv-file and longphase 'phase' manages to run and phase both VCFs.... BUT, because the STR VCF actually has one line per r…