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I've just noticed something very odd while observing the resulting VCF file (the first one, containing both linked and unlinked SNPs). For a given locus containing multiple SNPs (i.e. more than one po…
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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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Working with a large-ish dataset (30TB raw reads), and was wondering what a good strategy would be for working with the joint_germline option to get cohort SNP calls. Would it make more sense to try …
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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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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
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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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 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…