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Ratio of inbreeding coefficient to ROH is helpful to identify problematic samples during sample QC
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Hi Arun,
I want to run NgsAdmix and using inbreeding coefficients. I don´t understand how your scripts take in to account ibreeding coefficients. Could you plese tell me in which step you are inclu…
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Something simillar (https://github.com/magnusdv/pedprobr/issues/1) for the wish-list: simulation with inbred founders
``` r
library(pedtools)
library(forrel)
x = singleton(1)
m = marker(x, all…
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The below tells me that founder inbreeding is ignored by ibdsim2
and perhaps it should, but could notify user:
``` r
library(pedtools)
library(ibdsim2)
cou = doubleCousins(0,0) #remove 's'?
f…
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User Report:
Hi,
I've run into a frustrating problem: when lifting over certain VCFs from b37 to hg38, I'm running into LiftoverVcf exiting with errors like `Exception in thread "main" java.lang.Ille…
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This is probably obvious, but the documentation could
note that `exclusionPower` will hang if `n` is increased as indicated below:
``` r
library(forrel, quietly = TRUE)
n = 3 # hangs for large n,…
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It looks like gnomad_popmax_af doesn't match for some variants
https://gnomad.broadinstitute.org/variant/1-16902804-C-A gnomad_popmax_af looks to be 0.01492
Yet following gnotate with the grch37…
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Hello,
I have a question: Can discoal simulate non-random mating such as inbreeding/selfing?
I could not find a coalescence simulator that has such functions. Not sure if this is limited by the …
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Might be a basic question but I can not find the similarity command to build kinship matrix in pyseer 1.1.2 when installed using conda install pyseer.
`similarity --vcf snps.vcf.gz samples.txt > gg…
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I am running command: `spliceai -I 4-ZL2487_S31_L001_001.vcf -O 2487_output.vcf -R ucsc_hg19.fa -A GENCODE.v24lift37`
and getting warning:
```
Using TensorFlow backend.
2019-02-11 00:29:47.295…