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Hi!
First, let me thank you for releasing and maintaining shapeit4, and with setting aside time to contend with what usually amounts to user error on part of the community (which I will likely be gu…
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Copied from Slack:
![comparison-ibd-binned-1cM](https://user-images.githubusercontent.com/17755074/127788948-6db42d7b-d6af-432a-8df7-e7aabb9a7f7f.png)
> Hi Yan and Jerome, I wanted to talk more ab…
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Hi ~
Thanks for developing this handy program.
I am working on a haploid fungus and wondering if I can use this program as well.
I have 12 samples and generate these two files at last. It seems l…
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Hi, Lolita,
After running:
python3 SVJedi//svjedi.py -v $dir/Chr12.INS.CW01.seq.vcf -r nip -i reads.pass.fastq.gz -o $dir/Chr12.INS.CW01.gy -t 4 -d ont
I got this error:
Traceback (most recent c…
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Hello,
I'm trying to think of a way that I can use this tool to detect variants that occur more frequently in one group than another. For example, suppose I have 50 samples sequenced to 20X coverag…
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I'm trying to catch up on what's been going on in the world of alternat vcf representations and I'm trying to understand what the benefits of savvy are vs bcf. I've run into a few questions.
1. I…
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I have managed to generate a minimal bam file that reproduces the issue.
First of all, you have to download the mini input.bam file from this dropbox link: https://www.dropbox.com/sh/xae79hanumpire…
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Hello,
We have been computing ihs along the genome for a group of birds that hybridize. The populations here were chosen to contain 10 individuals each with non-hybrid individuals. An astonishing …
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Hi Peter,
In practice, it is frequent to perform a two-stage analysis:
1. get one BLUP per individual via a somewhat sophisticated mixed model (e.g. to account for spatial and/or temporal covari…
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We are planning to do an experiment in our lab which has 4 different individuals in one well. After applying souporcell I am looking for a way to correspond the clusters to each individual.
I read…