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It might be nice to be able to genotype on multiple SNP sets in a single run. I'm specifically thinking of pileupcaller here, not sure how it would apply to other genotypers, but:
Currently, the re…
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hello,teacher,my result that have a lot SNP loci which the FDR and P-value values are same,i think what one reason is that the genotyping results for some SNPs are consistent,while some SNPs with inc…
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We're trying to use SNParcher on some fairly large genomic datasets at the moment (2000 + individuals), and I am anticipating a lot of slow-down at genotyping steps. I was wondering if it's possible t…
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Hi there!
I have been working with simulated data using BridgePRS and I found that for exactly the same pipeline a phenotype returned an error due to differing number of dimensions. After some lon…
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Hi there,
I would like to use QuantiSNP to call CNVs from my genotyping SNP array but I cannot install it without the .exe file.
Could you please update the repository so the file can be download…
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Hello,
I find there are a fewer SNP overlap rate between the callset form pangenome-graph-from-assemblies and the GATK results. What could be the reason? The article seems to only compare the abili…
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Hi
I completed the genotyping of all samples (the previous error was not resolved, so I replaced one of the samples). After merging them, I conducted quality control. Unfortunately, the genotyping…
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Hi Giulio,
The array Finngen2 Axiom custom array from ThermoFisher was used for genotyping in our project. We would like to convert the .CEL files to a .vcf file to run the MoChA pipeline. We found…
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Testing has shown that some samples are not assigned any genotype based on the kmer scheme file but are correctly typed using the SNP scheme. This is likely the result of a missing partial assignment …
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Hi,
I have suggestions for "OBI:0000435" - "genotyping assay" term and some of the terms under it.
"Genotyping assay" has synonyms that include snp, which is limiting and confusing, so I'd remo…