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**CHM13V2 T2T Assembly**
```bash
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.fna.gz
snipe sketch --ref GCF_00…
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Options:
- [ ] Only Amplicons vs. semi-Amplicons: with only one primer hybridize due to partial sequences
- [ ] Min and max length of the amplicon
- [ ] Ta and max delta-G
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I'm having some issues with the calculateChromosomeRelativeCoverage function running with the tumor_cov object being addressed at a nonexistent index. What do you believe could cause this?
```
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I have a few WGS samples (matched T/N) at 80X with relatively high purity and have matched FISH showing ecDNA with the target gene. I ran amplicon architect suite with suggested inputs and the output …
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I would be glad to implement this pipeline to process my AMF LSU sequences from Illumina Miseq using the "AMF pipeline"; however, I have encountered an error while creating the AMF pipeline environmen…
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### Description of the bug
Viralrecon has worked perfectly for our SCV2 and some hybrid capture protocols (with the metagenomic side). However, when I ran the pipeline by passing a custom bed file an…
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Hi,
I am trying to run strelka2 in somatic mode on high depth data (~3570.95X) on a small gene panel (trusight) but the job never ends. I killed the job after 15h.
This is the command line that …
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Need to flag this up as coverage for this exon may not be reported
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Hello! My nf-core/viralrecon run was halted due to R version clash. Please see the error message below -
ERROR ~ Error executing process > 'NFCORE_VIRALRECON:ILLUMINA:PLOT_MOSDEPTH_REGIONS_AMPLICON…
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Hi, thanks for your contribution to the variation detection. I am using **VarDictJava**, and encountering some problems, hoping to get your help. The variant we want is not in the tbl file VarDictJava…