-
**Describe the bug**
In the output of `vcfwave`, the phased genotypes are not consistent with the input VCF.
**To Reproduce**
Here are some examples of the incorrect phased genotypes.
Inpu…
-
## Description
The [Genotype repository](https://github.com/Clinical-Genomics/genotype) has been partly replaced by [Genotype-api](https://github.com/Clinical-Genomics/genotype-api). All front-end in…
-
Add a modular ingest using our ingest cruft template that brings in genotypes and associations to genotype components
Already started at: https://github.com/monarch-initiative/alliance-genotype-ing…
-
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…
-
Hello @jzieve
I see some of the genotypes have empty ALT allele. This could be simply missing calls. But instead of using `.` or `N`, the field is simply empty. In other records I do see the ALT be…
-
Hi @freeseek
Following up on #68, I was wondering if it may be feasible for you to include an Illumina_genotype tag in the FORMAT field? I see that based on ALLELE_A/ALLELE_B and GT the illumina_g…
-
Hello,
First, I want to express my gratitude for developing xTEA.
I am encountering an issue while using xTEA’s case-control mode to identify somatic transposon (specifically Alu) insertions. Ba…
-
Here are all the genotype comments, with links to the genotype pages: [genotype_comments.txt](https://github.com/pombase/website/files/14771447/genotype_comments.txt)
Here are some examples:
…
-
It might be nice to be able to genotype on multiple SNP sets in a single run. I'm specifically thinking of pileupcaller here, not sure how it would apply to other genotypers, but:
Currently, the re…
-
老师您好。我运行示例的数据的时候没有问题,但运行自己的数据会报错:
我的Genotype 文件并不是从hapmap转过来的,而是重测序生成的vcf文件直接用plink转过来的,不知道是否会有影响?谢谢。
Extracting number of samples and rownames from Genotype.fam...
Extracting number of variants an…