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test_plink for PLINK
a. binary PLINK output
b. binary output + input
c. pedigree
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A useful feature to have would be to honor pre-existing phase.
Typically sources of pre-existing phase are
1) pedigree relationships : duo's, trio's, half-sib sire families
2) 10x Chromium long ran…
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Java noob here. Trying to compile and use Pail examples from Big Data book on Ubuntu 14.04. Below is the full output. Any and all help greatly appreciated! I'll continue to try and figure out. @handdo…
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I've already simulated 22 autosomes for ~1.5M samples using the [`FixedPedigree`](https://tskit.dev/msprime/docs/latest/api.html#msprime.FixedPedigree) model and I'm wondering about how much work migh…
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Dear developers,
I would like to express my gratitude for providing such a useful tool, mpMap2. I am currently working on constructing a linkage map for a 16-parents MAGIC population that was gener…
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I've been running into an issue where running the Kinship function, I run into this error message.
```
ArgumentError: The pedigree data file does not contain a field
labeled Person or Individual…
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the file path in JSON file should be more fixable
example:
"/home/yindong/R/x86_64-pc-linux-gnu-library/4.0/simer/extdata/05others/pedigree.txt" should be replaced by "${users r path}/simer/extdata/…
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Hi
In my output from somalier on 4 related individuals (illumina wgs data), i do not get any pedigree inference, as described in https://github.com/brentp/somalier/wiki/pedigree-inference
What am I …
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How do we specify pedigree information for families or trios for multisample calling mode?