armartin / ancestry_pipeline Goto Github PK

Hi,

Would you be able to provide the Makefile for RFMix, so to execute the RFMix software?
I would really appreciate that because I am unable to run PopPhased.

Thanks,
-Fred

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.

Is it one column containing the end position?

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.
Thanks

Hi, was wondering if someone had a tip for generating ancestry karyograms using RFMix2 outputs. I am trying to use ExtractTracts.py to convert my RFMix2 outputs into vcf files and then convert them into .bed files. However, I am unable to split the vcf files into 2 separate files, 1 for each chromosome. Would appreciate any pointers/work arounds for using RFMix 2 results!

Hello ,Can you provide RunRFmix.py for me to study? I can't find it in your code. Thank you very much.

Hi Alicia,

First, I thought it might be nice to point out that I was referred here from another site (for the chromosome painting portion of your scripts):

slowkoni/rfmix#9

Second, I noticed that you provide a link to download the genetic map files used by RFMix. I'm guessing those are within the .tgz files (which I am working on downloading).

Just out of curiosity, did you know of a direct link to those genetic mapping files? I was having some difficulty finding them within a subfolder of the FTP, but that doesn't mean they aren't there somewhere.

I would guess that you already know about it, but I did find this HapMap file (from a Biostars discussion):

https://ftp.hapmap.org/hapmap/recombination/2011-01_phaseII_B37/

However, I'm guessing what I can download from 1000 Genomes will cover more sites (but something like that smaller file is what I am looking for).

Best Wishes,
Charles

Hi,

Where can i found RunRFmix.py?

Thanks in advance

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? Can you give an example? Does it look like the following?

21 100 200 EUR
21 200 800 AFR
...

One .bed file for hap1, and the other for hap2?

Thanks so much!

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?

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 are using a copy of the incorrect model in this repo, and so I am opening this issue to alert you.

Please see here for details on what the error is, and what actions you can take to fix it.

We have also written a short note analysing this and another related error, detailing the likely effects on downstream analysis. Thankfully, the differences between the misspecified model from msprime's documentation and the intended model are slight.

I apologise for this error and I sincerely hope that it has not affected your research.

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 "ancestry_pipeline/shapeit2rfmix.py", line 263, in
main(args)
File "ancestry_pipeline/shapeit2rfmix.py", line 131, in main
sample_indices.append(find_indices(ref_set, open_shapeit(sample), out_sample))
File "ancestry_pipeline/shapeit2rfmix.py", line 46, in find_indices
raise RuntimeError('Shapeit sample file appears to be incorrect')
RuntimeError: Shapeit sample file appears to be incorrect

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 flag "--ref_keep" and "--admixed_keep" take. The previous steps do not generate any file with ".ref" or ".notref". So what are these files and how can I prepare these files?

Thanks much!

shapeit2rfmix.py has no way of knowing how to separate reference panel individuals. Add a flag to specify reference individuals.