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Documentation on the fastsmc map file (https://github.com/PalamaraLab/ASMC/blob/main/docs/fastsmc.md#genetic-map-map) are unclear:
> The genetic map file needs to provide physical positions (in bas…
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The current definition of 'variant collection' in SO is “a sequence collection comprised of one or more sequences of an individual”.
A. It is not clear what is meant by ‘of an individual’ . . . this s…
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I installed SNPBac in a conda environment built in python 2.7 and installed all other dependencies as one conda build. (Gubbins would not install with error stating that I am not using the right conda…
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I am writing this post to suggest a neat new feature that could be added to this module: the addition of variety through simple genetics.
Currently, plants in the SimpleFarming module have very fix…
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`phase_rare` is failing while attempting to index the output, with errors like the following printed to stderr across all chunks:
```
[W::bcf_record_check] Bad BCF record at 28101822: Invalid CONT…
BEFH updated
11 months ago
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Hi
Just wondering about the format for the input snp_list? I have SNPs from a fine-mapping project that I'd like to test. Neither a 3 column, a 4 column BED file, with or without a header line see…
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Proposal, Task 3
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Initial notes on proposed scope and definition of these VA type, based on requirements and considerations documented [here](https://docs.google.com/document/d/1J4AqGDEqyK8KAzfiowgHYKJNvzHuwHSHgkN9dleL…
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Hi, I'm getting a shapeit4 issue during the first burn-in iteration
g++ Version:
`$g++ --version
g++ (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
Thi…
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Hello, I'm getting a cryptic error that I believe is related to reading the groupFile. The groupFile is properly formatted, so I don't know who could be causing the typing error.
Here are the most r…