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Hi @jzieve,
As a fix to #78, I might need to use a different csv beadpool manifest version than the orignal manifest used to generate idat/gtc. Many of new manifests will have fewer loci than the m…
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Hi,
For strategy 2, you recommend subsetting the donor VCF file as below. Specifically how would you recommend to filter out SNPs with "too much missing values" or "genotypes too similar across don…
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Hello @anglixue,
I have been trying to run mtCOJO on a trait, adjusting for 3 other traits using GCTA v1.94.1 and this is the error message I received:
```
Error: the variance-covariance matrix o…
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Hi,
I'm using a genomic data set with 180K SNPs to create G matrices. I want to exclude around 3K of these SNPs from the calculation, so I used the j argument to include all other columns than the…
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**What is the SO term name and accession?**
SNP (SO:0000694)
**Describe what you would like to change.**
Drop the frequency requirement and change the definition to
> SNPs are single base …
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Hello,
I ran cellsnp-lite with the following command for calling variants in mitochondrial transcripts in 10X scRNAseq data and for each of three independent samples, received 16,299 variants, which …
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Dear GAPIT Support Team,
I am encountering a persistent issue with GAPIT. Although version 3.5, which is intended to fix certain bugs, is mentioned on the website, I am still using version 3.4. GAP…
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Unattended upgrade process can lead to flakes like this on the pipline **`kata-containers-CCv0-ubuntu-20.04_snp-x86_64-CC_SNP_CRI_CONTAINERD_K8S-PR`**:
```bash
...
12:03:12 E: Could not get lock …
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Hello, I converted the allele frequencies from the reference panel to MAF and incorporated them, but it identified MAF as "Allele frequency." Is this correct? I would appreciate clarification. Thank y…
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Hi there,
I am currently running the find_intersecting_snps.py script from step 3 of the mapping pipeline, but it is taking a very long time to run - currently outputting the bam/fq files only up …