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**Background**
I have a pedigree file with roughly 35,000 rows and around 700 families. The file looks something like this
```
...
fam20,5101470,5101420,5101410,M,0
fam20,5101340,,,F,0
fam20,5…
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Om du kan får du gärna skicka med även denna flagga med pedigree/family informationen.
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In a case of[ Pedigree collaps](https://en.wikipedia.org/wiki/Pedigree_collapse)e one ancestor is displayed with both parents, while second ancestor is displayed without any parents.
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The pedigree analysis workflow is hooked into the `analysis` subcommand which is too ambiguous in meaning.
It should be more like `pedigree_analysis` or `pedigreeanalysis`, but the two-word subcomm…
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Thank you for your code! I have a quetion for visPedigree. The program checks the pedigree for loop, but how does it know where loop are present?
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Hi Whatshap team,
I'm having trouble running whatshap to phase a VCF file with 5 or 6 samples in a pedigree mode. The VCF file has around 21 million variants and I have families with 3, 4, 5 and 6 …
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Dear Dr. Wang,
SEQLinkage has great power compared with single variant linkage analysis. We plan to use it in WES data on 8 samples within a family.
The problem is that when we generate region …
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When looking at the log for ligate I noticed something that doesn't seem right. It appears that when using a pedigree, it prints the file name from the file listing the chunks to ligate rather than th…
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Evaluate whether it's possible to use non-unique IDs in a pedigree, i.e. having the same IDs in different families.
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Hi,
I tried running AlphaImpute2 with the following code:
AlphaImpute2 -genotypes data/Genotypes_all.txt\
-pedigree data/ped_certain.txt \
-out outputs/ai2_SW_geno -wri…