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Hi paturley,
There is no freq column in my summary data. I see that in other posts, you mentioned using the reference population to calculate MAF. I used 1000G data to limit SNP to SNP in summary, …
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```
founderGenomes
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# Context
See [**cell-sci-data-wrangling**](https://czi-sci.slack.com/archives/C024HCSH9PT/p1714423152483169).
# References
* [International Mouse Strain Resource (IMSR)](https://findmice.or…
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Hi! Dr. Dou,
Thank you for developing this great software Monopogen for both germline and somatic SNVs detection in single-cell sequencing data. We found it very efficient in somatic mutations call…
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we have:
v101 -> Jump to Variant 101
a101 -> Anaylsis 101 or Allele 101
Didn't mean to do this, not sure when Analysis shortcut got in there
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Can you clarify what "incompatible allele" means versus ambiguous, palindromic (inferrable), palindromic (not inferrable) or incompatible allele frequencies?
Removing the following SNPs for inco…
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It's pretty helpful for teaching purposes to be able to demonstrate small _tsinfer_ input files without needing a VCF. I wonder if we could define a class method like this:
```python
class Variant…
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Hi,
I'm getting the following error when trying to joint call some gVCF files:
```
[14707] [2023-11-09 18:40:20.654] [GLnexus] [error] mother_snv.g.vcf.gz Invalid: allele is not a DNA sequence (…
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Converting `allele varchar(1024)` column in `AlleleFreq` table to `allele_id serial` (defined in `Allele` table) will reduce the data size for `AlleleFreq` table.
knmkr updated
8 years ago
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The error below seems to be arising from some software version incompatibility ? but it is not clear what. bowtie log is not empty, and bowtie version is 1.3.1
The digital haplotype is written into…