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admixfrog's Issues

KeyError: "['NEA'] not in index"

Hi,

I would like to use admixfrog on my samples. I am testing it with known samples from the 1240K SNPs datasets (https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data) so my input is in eigenstrat format.

It is not clear to me if I cannot use preliminary analysis to get target and reference files when using data in this format.

However, I tried to launch the command line in a similar way to the one you suggest as quickstart

admixfrog --gfile v44.3_1240K_public --target UstIshim_snpAD.DG --states NEA=Vindija.DG+Altai.DG YRI=Yoruba.DG Denisova.DG --cont YRI --out quickstart
I got this error

Traceback (most recent call last):
File "/home/student6/anaconda3/envs/python38/bin/admixfrog", line 8, in <module> sys.exit(run())
File "/home/student6/anaconda3/envs/python38/lib/python3.8/site-packages/admixfrog/interface.py", line 454, in run run_admixfrog(**V, **algo_pars, **geno_pars,
File "/home/student6/anaconda3/envs/python38/lib/python3.8/site-packages/admixfrog/admixfrog.py", line 402, in run_admixfrog df, df, sex, tot_n_snps = load_admixfrog_data(target_file = target_file,
File "/home/student6/anaconda3/envs/python38/lib/python3.8/site-packages/admixfrog/admixfrog.py", line 239, in load_admixfrog_data df = read_geno_ref(fname=geno_File, pops=state_dict, 
File "/home/student6/anaconda3/envs/python38/lib/python3.8/site-packages/admixfrog/geno_io.py", line 173, in read_geno_ref  Y = read_geno(*args, **kwargs)                                                                                                       
File "/home/student6/anaconda3/envs/python38/lib/python3.8/site-packages/admixfrog/geno_io.py", line 107, in read_geno Y = Y[set(pops.values())] 
File "/home/student6/anaconda3/envs/python38/lib/python3.8/site-packages/pandas/core/frame.py", line 3030, in __getitem__indexer = self.loc._get_listlike_indexer(key, axis=1, raise_missing=True)[1]                                                         
File "/home/student6/anaconda3/envs/python38/lib/python3.8/site-packages/pandas/core/indexing.py", line 1254, in _get_listlike_indexer 
indexer,keyarr=ax._convert_listlike_indexer(key)                                                                                 
File "/home/student6/anaconda3/envs/python38/lib/python3.8/site-packages/pandas/core/indexes/multi.py", line 2568, in _convert_listlike_indexer
raise KeyError(f"{keyarr[mask]} not in index")
KeyError: "['NEA'] not in index"

Could you please help me?

Thanks.

BW,
Maria Angela

PanTro4 reference

Hi,
How was the pseudo haploid panTro4 reference sample created for the reference file?
Thanks,
Chen

dating of admixture

Hi,

I see from your preprint and other published works that introgressed fragments called by admixfrog can be useful to estimate the dating of admixture. However, the methodology is not very clear to me (please find attached what I see from your preprint).

Could you please suggest how to proceede with the analysis after an admixfrog run?

Thanks.
BW,
Maria Angela
Peter_screenshot

Reference File Creation for Camelids

I want to create a reference file to determine the ancestry of ancient camelid samples I have. I want to consider two ancestral populations: the guanaco and the vicuña. My approach is the following:

  1. Create a .vcf using the command

./angsd -b list.list -dovcf 1 -gl 1 -dopost 1 -domajorminor 1 -domaf 1 -snp_pval 1e-6

where list.list are my samples (3 from guanaco, 3 from vicuña, and 1 camel to act as an outgroup).

  1. Use this .vcf in the command:

admixfrog-ref --vcf [output] --out x.ref.xz \ --states GUA VIC \ --pop-file data.yaml
where the .yaml file looks like:

`GUA
-GUA_Sample1
-GUA_Sample2
-GUA_Sample3
VIC
-VIC_Sample1
-VIC_Sample2
-VIC_Sample3

pseudo-haploid
-Camel
`

which will output the reference file.

Have I understood this correctly? What I am confused by is that the STATES in the provided code in the documentation do not match those in the .yaml file.

Any help would be greatly appreciated!

admixfrog-bam NotImplementedError

Hi,

I would like to generate admixfrog input from my BAM file, after generating reference.xz file.

This is the command launched

admixfrog-bam --bam sample_rmdup.sorted.bam --ref afr_nea_ref_samples.xz --random-read-sample --chroms 21 --deam-cutoff 3 --minmapq 30 --length-bin-size 35 --out sample.in.xz > admf_in.log 2> admf_in.err

However the process exits after a few seconds with this error

...
[18:20:31]:  Filter is {'deam_only': False, 'pos_in_read_cutoff': 2, 'min_length': 35, 'max_length': 1000, 'minq': 25, 'minmapq': 30, 'report_alleles': False}
Traceback (most recent call last):
  File "/home/student6/anaconda3/envs/python38/bin/admixfrog-bam", line 8, in <module> 
    sys.exit(bam()) 
  File "/home/student6/anaconda3/envs/python38/lib/python3.8/site-packages/admixfrog/interface.py", line 141, in bam
    process_bam(**args)
  File "/home/student6/anaconda3/envs/python38/lib/python3.8/site-packages/admixfrog/bam.py", line 200, in process_bam
    cov = AdmixfrogInput( 
  File "/home/student6/anaconda3/envs/python38/lib/python3.8/site-packages/admixfrog/bam.py", line 27, in __init__
    raise NotImplementedError
NotImplementedError

Could you please help me?

Best wishes,
Maria Angela

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