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Hi, I am working with Aldy and need to provide --phase parameter for more accurate calling of novel star alleles.
I used HapCUT2, based on the related documentation and received both "haplotype_outpu…
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**Context of the feature request related to a problem:**
We would like to better model MONDO biological inheritance (see https://github.com/monarch-initiative/monarch-ingest/issues/295)
**Workin…
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**1. What were you trying to do?**
Mapping short reads to reference and genotyping SV
**2. What did you want to happen?**
ERROR: Signal 6 occurred. VG has crashed
**3. What actually happen…
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This looks like a comprehensive workflow. I'd like to use it to do DE analysis and variant calling for other species, like non-human malaria. What would I need to do to make that happen?
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Hi,
After calling inStrain profile (version 1.4.0), I have this issue which causes some SNVs that are intergenic to have no mutation type annotated as "I". For example, the following output:
scaff…
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## Describe the issue
I have an issue regarding the output of the vep offline as it's not getting me the Gene Symbol as I used to have on the online platform. Although I changed the output format usi…
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Hi team,
Use sniffles v2.02 in my latest analysis, after calling SVs for each sample with sniffles, I merged all the snf files using command
` sniffles --threads 24 --input *.snf --vcf merg…
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Brief description of the problem
I have an RStudio Server instance running on a GCP VM. I'm getting the following error
``` r
library(tidyverse)
library(magrittr)
#>
#> Attaching package: '…
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I had a question regarding using WhatsHap to phase PacBio Hifi long reads after using both DeepVariant and GATK for the variant calling.
I was making a trial to see if there would be a difference b…
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Let us consider the following situation, where
_u1,u2,u3,u4,u5 are UMI sequences, u1,u2,u3 group together as the same UMI, and u4,u5 form the other UMI_
_the sequence following the : is the "am…