mocksu

My VCF contains virtually no 1/1 genotypes

1

I have 1060 WGS samples and I used MToolBox V1.1 to call MT variants. When looking at the result VCF file, I noticed that my GTs are either 0 or...

On the page https://chr1swallace.github.io/coloc/articles/a06_SuSiE.html, there is a paragraph like this: > With these susie output objects stored, we can colocalise every pair of signals. This analysis says the first pair,...

For coloc, we have 5 competing hypotheses: H0: no causal variant H1: causal variant for trait 1 only H2: causal variant for trait 2 only H3: two distinct causal variants...

What's the format of the bed file for plotting?

1

The manual has the following command to plot IND='HG02481'; python plot_karyogram.py \ --bed_a ${IND}_A.bed \ --bed_b ${IND}_B.bed \ --ind ${IND} \ --out ${IND}.png What's the format of the .bed file?...

shapeit2rfmix.py --ref_keep --admixed_keep values

7

The README is great, and I have been able to smoothly follow from the beginning all the way to shapeit2rfmix.py. For shapeit2rmfix.py, it's not clear to me what values the...