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Hello Dr. Li,
Thanks again for this great package. I have a quick question that why some cMAC output has decimal points. Based on my understanding, this might be caused by the genotype imputation,…
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Hi,
when i used the vg call to obtain the genotype file from short reads. I didn't know these genotype. for example,1/1,1/0,0/1 . These genotype were not including 0/0?
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Dear Armando,
I encountered this error with example data:
DIVIDE .ped AND .map FILES IN CHROMOSOMES
RUNNING ANALYSIS OF CHROMOSOMES ...
xargs: bash：以状态 255 退出；中止
CHROMOSOME ANALYSES took 55 s…
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@sandve, I am working on reconstructing a haploid haplotype using the imputed genotypes from KAGE. Currently, I am using the following commands:
```bash
kage index -r MHC-CHM13.ref.fa -v MHC_49-M…
gsc74 updated
2 months ago
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Hi!
I'm interested in exploring LAVA to estimate heritability for specific loci across multiple ancestries but for a single phenotype.
Is this an option? If so, is there a provision to input multip…
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The genotypes in a GWAS are ambiguous because they encode the number of A2 allele in the BED file (see https://openmendel.github.io/SnpArrays.jl/stable/) which could be either the minor or major allel…
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Hi,
I have a VCF that was processed with [HiPhase](https://github.com/PacificBiosciences/HiPhase). The file contains lines with "|" as well as "/" for the `GT` value. Example:
```
chrX 1189233 …
rollf updated
1 month ago
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As part of our [genotypes and variants super ticket](https://github.com/monarch-initiative/monarch-app/issues/715) we identified that we want to confirm that our pipeline that brings in genotypes from…
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In light of https://github.com/samtools/hts-specs/issues/756 and further discussion with implementations, it appears that the current definition of GQ is problematic.
`GQ (Integer): Conditional gen…
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We are particularly interested in calculating SNP (Single Nucleotide Polymorphism) expression levels using single-cell ATAC data. We have utilized the Monopogen tool to compute genotypes associated wi…