peddy

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Parallel processing blocked

1

I've run into an issue trying to parallelize code using Peddy. I'm parsing a PED file and VCF, then splitting all variants into groups to process. This splitting makes it...

MattWellie

Runtime for large datasets.

4

Hi, I am trying to generate some cohort metrics for QC steps via peddy. My sample size is about 187000. I have provided the gz zipped VCF and fam (PLINK...

sdsilva10

Report which variants were used?

1

Hi, Is there an easy way to determine which variants in a vcf were used by the ancestry classifier? I could write a script to do this with the included...

bhanratt

check Y chromosome

2

might help resolve samples that are ambiguous from just looking at X.

brentp

PCA projection - strange population classification

3

Hi, I am analyzing a kindred - two parents and two kids. The PCA projection of the samples is attached below. Mother is the sample of clearly EU ancestry, PC2...

numicator

Peddy run error: AttributeError: 'DataFrame' object has no attribute 'ix'

2

Hi , everyone, I install peddy through conda [ conda install -y peddy ] 1. $ python -m peddy --plot -p 4 --prefix merge4fam merge4fam.vcf.gz merge4fam.ped VCF header: #CHROM POS...

yusmile0618

Python version and libraries version incompatibility due to drop support for python 2.7

2

Can you provide exact version of the libraries in requirements.txt. Because numpy and all libraries that are build atop of it crash during installation because newest version of those libraries...

NikolaBio

Running Ancestry Analysis on Samples with no Hets Found

4

Hi @brentp! I'm working on a project trying to run some ancestry analysis on single-cell RNAseq samples. I used monovar for the variant calling and then peddy for the ancestry...

angelussong

Library not loaded: @rpath/libdeflate.so

1

Hello. I created an environment with conda with python 2.7 on macos mojave. Entered the command: `pip install peddy` And got an error: `Traceback (most recent call last): File "/Users/nail/miniconda3/envs/peddy/bin/peddy",...

maksjutov

incorrect expected relatedness for consanguineous family

6

I have a family where the parents are first cousins. I gave Peddy an extended pedigree and it was able to distinguish the parents as cousins, which matches the calculated...

ekarlins