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Is there a way to increase the visibility of SNPs at wider views? In the example below, I can see SNP differences between alignments in a 56 kb window, but not in a 140 kb window, which encompasses th…
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I would like to visualize the variants of the recombinant, donor and receptor, just as it is shown in the RIVET's web page.
However, whenever I run it locally in my computer and select one row in the…
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Hi there!
I am trying to mtCojo analysis on Alzheimer's Diseases by conditioning on Small vessel disease by running this:
gcta64 \
--mbfile 1000G_EUR_Phase3.mtcojo_ref_data.txt \
--mtcojo-file…
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How to choose SNPs as the input for alleleCount? More specifically;
1. How many SNPs are sufficient throughout the genome?
2. How should the SNPs be distributed along the genome? i.e. in terms of …
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Hi MESuSiE developers,
Thank you for developing such a powerful tool for fine-mapping across multiple ancestries. I have two related questions that I hope you could help me with:
Handling Multip…
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LDtrait(
snps=snps,
pop = "ALL",
r2d = "r2",
r2d_threshold = 0.1,
win_size = 5e+05,
token = "my token",
file = FALSE,
genome_build = "grch37",
api_root = "…
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I have been using a core genome alignment as input of grapeTree stand-alone version, but it crashes when the alignment contains too many sequences because of a memory issue (I do not have enough memor…
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Hi,
I'm having trouble finding SNPs overlapping with reads using BAM files generated with BD Rhapsody pipeline. I specified UMI tag (MA) manually and cell barcode is the same (CB). However, the cou…
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Dear Armando,
In my own data.map file, there are 1812799 SNPs on chromosome 1, out of a total of 40 chromosomes and 8495844 SNPs. Is this data not runnable?
![image](https://github.com/user-attachme…
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Firstly, thank you for creating such an amazing tool! I am plotting the results of collapsing gene analyses and in my "top" datasetmy top two genes have associations of 10e-300 and then the next most …