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AlexTISYoung/snipar
Install problem/question

Hi there, I have been attempting to install snipar on my university s hpc. I have used conda to install conda create -n sniparenv python=3.9 scipy conda activate sniparenv pip install snipar Things appear ...
  • grbs27
  • 1
  • Opened 
    on Dec 9, 2024
  • #34

AlexTISYoung/snipar
Issue with Calculated Scores and Effects in snipar

Hi there, First of all, I d like to express my appreciation for creating the snipar tool – it s been incredibly valuable in my research. However, I ve encountered some discrepancies when using snipar ...
  • PandaPowell
  • 7
  • Opened 
    on Aug 31, 2023
  • #31

AlexTISYoung/snipar
Memory Allocation Error in impute.py

Hello, I am attempting to run impute.py in a conda environment with Python version 3.9.16, pandas version 1.1.4. I am encountering the following error: 2023-06-27 19:22:09,875 INFO impute - main: creating ...
  • AnnabelPerry
  • 4
  • Opened 
    on Jun 28, 2023
  • #29

AlexTISYoung/snipar
KeyError: 'InfType' in impute.py

Hello, I am attempting to run impute.py in a conda environment with Python version 3.9.16, pandas version 1.1.4. I am encountering the following error: 023-06-27 14:22:47,023 INFO impute - main: creating ...
  • AnnabelPerry
  • 3
  • Opened 
    on Jun 27, 2023
  • #28

AlexTISYoung/snipar
ibd.py genetic map errors

Hello! Thanks for making this software - it s incredibly exciting! I m troubleshooting some errors ibd.py which relate to the genetic map and was wondering if you could help. Here is a full description: ...
  • AnnabelPerry
  • 4
  • Opened 
    on Jun 21, 2023
  • #27

AlexTISYoung/snipar
IndexError: index 3 is out of bounds for axis 2 with size 3

Hi there, Thank you for writing this, I have been trying it and it s been working mostly well. I have encountered this error while trying to run impute.py: $ impute.py --bgen /path/to/data.chr_@ --ibd ...
  • GiulioCentorame
  • 2
  • Opened 
    on May 26, 2023
  • #26

AlexTISYoung/snipar
Error：Less than 50% of SNPs have genetic positions in genetic map file

Hi there Thanks for your excellent work on the development of this useful tool! I got an error when used it in my family data as follows: $ ibd.py --bgen chr1.phased --pedigree pedigree.txt --map geneticmap1000G_chr1b37.txt ...
  • sherryfan030
  • 3
  • Opened 
    on Dec 8, 2022
  • #24

AlexTISYoung/snipar
Include source distribution in PyPi

Hi there, I would like to make a conda build for snipar, but the PyPi repository is missing the source distribution. Would you be able to add the source repo to it by any chance? The alternative would ...
  • GiulioCentorame
  • 1
  • Opened 
    on Oct 5, 2022
  • #23

AlexTISYoung/snipar
Imputing missing parental genotype

Hi there I have a question. I have genetic data of female parent, F1s, but missing the male parent. How can I proceed to impute the missing parent data? Do i need to calculate IBDs first. My data is in ...
  • jtahir
  • 3
  • Opened 
    on Sep 5, 2022
  • #22

AlexTISYoung/snipar
Installing on M1 Macbook Pro

When trying to install SNIPAR on a macbook pro with an M1 chip, I get the following error for both python 3.8 and 3.9 (it is more complicated to install python 3.7 and older on an M1 mac). (env) mbp % ...
  • michaelbennett99
  • 1
  • Opened 
    on May 6, 2022
  • #17
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