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A high-level overview of major new features in VRS 2.0 would help with orientation.
Create documentation for the following major new features:
- [ ] Descriptive metadata
- [x] GA4GH Keys
- [x] S…
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Hi, I'm assembling a highly heterozygous plant genome with HiC data and the haplotype assemblies are very different sizes, which like the problem encountered in [https://github.com/chhylp123/hifiasm/…
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Hello, I ran "selscan --xpehh --vcf vcf1_Chr1.gz --vcf-ref vcf2_Chr2.gz --pmap --out outfile", but no files were generated.
The result of the operation is:
selscan v1.3.0
Opening vcf1_Chr1.gz...
L…
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Hi,
This follows the issue #80
The problem was the group assignment to the chromosomes homologous groups. We are working on the assembly of a tetraploid potato. If we do not separate the contigs i…
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Create another haplotype module with PEHaplo - a de novo assembly haplotype reconstruction tool (and apparently easier to install program).
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hello
I have assembled two haplotypes using the hifiasm software based on HIC hifi ONT data. I am wondering if it is possible to utilize this software to inspect errors in the haplotype assemblies. I…
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Dear @alexdobin,
I've noticed that reads that are assigned to haplotype 2 by STAR diploid are not processed in the same way as haplotype 1 reads by STARsolo. For instance, I am fairly confident tha…
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Low priority, but we should start thinking about this. learners/reference.md is a place to put a glossary. Then I think that we can link to the file somehow in our lesson.
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### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
Haplotype 1:
- Chamaecrista/fasciculata/genomes/ISC494698.gnm1.8Q19
- Chamaecrista/fasciculata…
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Hi all,
I am trying to call variants using the pggb singularity pipeline starting from multiple haplotype-resolved genomes. I used PanSN-spec naming and it all worked well until I had to chose the …