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Expected Behavior
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For Bugs:
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### Environment
#### Steps to Reproduce
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Hi, when I running the smc step, I find there are some warnings in the 'smc_out.vcftool.log' file.
$ grep "arning" smc_out.vcftool.log
Warning: Input is unsorted, results may not be complete.
War…
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**1. What were you trying to do?**
After building a plant graph pan-genome of with Minigraph-cactus, I used vg to map short reads to graph and genotype.
Details are as following link (Part 4: G…
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### Due date for Sprint 11 - May 16th.
### General
- [x] Improve installation instructions so that the annotator can be installed without issue on Amazon Linux 2023 - @dlin30 - 2024/05/08
### Prote…
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Hi everyone,
Im trying to get started with eager and I found this problem, in fact Im brand new with nf-core pipelines and I dont know if this issue is easily fixable. I recently installed nextflo…
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This issue serves as a discussion hub for development around a pipeline for benchmarking SVs. Development currently is happening on the [rm_benchmark_svs](https://github.com/broadinstitute/palantir-wo…
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## Description
Sessions are currently handled in a non-standard and non-explicit way in cg, which risks causing issues with incomplete transactions etc.
The main issues consists of:
- Sqlalchemy …
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Hi.
I first map the paired end reads to `.vg` graph. Then use vg surject to convert the `.gam` file to `.bam` file. Then I use `graphtyper `to do genotyping. But there is an error: `Reads with name=d…
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Hi,
I want to genotyping the chr21 using command:` graphtyper genotype GRCh38#chr21.fa --sam=chr21.sorted.bam --region=chr21`.
But there seems to be something wrong with it. The result only contain…
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The table on https://covariants.org/shared-mutations shows the shared aa substitutions caused by shared nucleotide mutations; amino acids aren't subject to mutation, only nucleotide sequences. It woul…