-
Hi,
I'd like to run iSAFE on a single chromosome (6), containing ~70K individuals, 35,863 SNPs covering 170Mb. I've been trying lots of different parameter settings of different window sizes, minim…
sahwa updated
2 years ago
-
The current VCF spec allows for a `*` allele (no brackets):
> "The ‘*’ allele is reserved to indicate that the allele is missing due to a upstream deletion."
CollectVariantCallingMetrics treats …
-
I am facing some errors with some of my runs (while some runs with other parameters or GWAS files have been successful). The first error instructs me to remove a folder with the clump results and then…
-
Hi
I'm using this tool and I noticed that it supports implicit phasing. Could you please clarify how implicit phasing differs from the standard (explicit) phasing? Additionally, is it possible for …
-
```
>>> import sgkit as sg
>>> ds = sg.simulate_genotype_call_dataset(n_variant=10, n_sample=2)
>>> ds
Dimensions: (alleles: 2, ploidy: 2, samples: 2, variants: 10)
Dimensions witho…
-
Hi! I am using lcWGS and some of my sites have zero read depth and thus the GL is not computed during calling. I am unsure how to handle these sites when converting to Beagle format. How is NGSremix e…
-
MGI:5759474 found [here](https://monarchinitiative.org/genotype/MGI:5759474). I thought it was odd that there were no phenotypes so I tried looking at the source but it failed; even a google search fa…
-
When subsetting a vcf file, it would be useful to trim all alleles from a multiallelic site that are not present in the samples being subsetted on. For example, consider the following entry
1 1…
-
@peteryzheng I have seen a couple of times inconsistent labeling from filter_reads.R, can you please check to make sure the same criteria is used overall.
-
Dear Florian
Firstly, I'd like to thank you for developing a robust PRS method, SCT.
I am reproducing the result of 'Making the Most of Clumping and Thresholding for Polygenic Scores'. However, …