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This issue aims to model simulation agent parameters using a DNA and genes-inspired approach. By structuring agent parameters, such as “learning rate,” as genes within a genome, we can encode, decode,…
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I have array genotypes and thus most of Y loci are no known, is it possible to improve algorithm so that it will not assign the wrong haplogroup? For example, our population have no N1a individuals, y…
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Hi @lrauschning,
when I run `msyd call` in `--core` mode on some potato haplotypes, I get a nice PFF file of the coresyn regions and a merged VCF for the same coresyn. The SNPs and indels which do …
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Hi,
I ran HiC-Pro v3.1.0 on Micro-C data, but I get about 30% alignment using default settings for `bowtie2`. Do you know what could be the issue? The index was generated using `bowtie2-build` on a…
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Hi,
I am a new user of the `coloc` package and need clarification on how to correctly set up input parameters, particularly `MAF`, `N`, and `sdY`. I am working with GWAS and eQTL data, where the GW…
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Usher SARS-CoV-2 masks quite a lot of sites (I think around 270, i.e. almost 1% of genome) based on this vcf: https://raw.githubusercontent.com/W-L/ProblematicSites_SARS-CoV2/master/problematic_sites_…
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Dear developers:
I was wondering that how to prepare a VCF for vartrix if I want to get variation information for a specific region per base.
For example , I want to get all variation information f…
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Currently, for MSK IMPACT, we have mutations, CNAs and fusions/SVs, but we have many additional types of derived data generated by CMO.
- Mutational signatures
- HLA types
- HLA LOH
- Genomics-i…
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Maybe do #758 first/same time
Anna B suggested:
* [Cancer hotspots](https://www.cancerhotspots.org/#/home)
* Onco KB (already there but not as quick links)
* Cancer bio (confirm link?)
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Hi Brad,
I am assuming the recall jar uses optimized parameter settings for the variant caller based on bcbio settings. I've been looking at exploring incremental join calling on tumour only samples.…