ancestry_pipeline

ancestry_pipeline copied to clipboard

Hi, Where can i found RunRFmix.py? Thanks in advance

bgyuris

Hi, was wondering if someone had a tip for generating ancestry karyograms using RFMix2 outputs. I am trying to use [ExtractTracts.py](https://github.com/Atkinson-Lab/Tractor/blob/master/ExtractTracts.py) to convert my RFMix2 outputs into vcf files and...

DavYang

rfmix2

3

Is it possible to use rfmix2 in this pipeline and/or its results as input for rfmix2plink. It would have been easier if there was a toy example for this pipeline....

mfazel

Shapeit2 Sample Input

2

I am setting up this pipeline to find local ancestry. I don't know why I am getting this error. Below is the error message. Traceback (most recent call last): File...

boratonAJ

What is the format for --snp_locations file?

1

Is it one column containing the end position?

rozaimirazali

cont_pulse_model_unif_params module not be found

1

I could not find the cont_pulse_model_unif_params.py in your or tracts' repository github page when testing tracts step, where should I download it? tks.

04linsi

We have recently learned that there was an error in the description of the Gutenkunst et al model provided as an example in the msprime tutorial. It appears that you...

jeromekelleher

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?...

mocksu

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...

mocksu

Im new in this kind of analyses but I not that all chromosomes get 3 columns in centromeres.bed file, except for chr 12,13,15,21,22, that is right?

hgarciaortiz