Issues

• How to assess the significance of fdM values from ABBABABAwindows.py?

  simonhmartin/genomics_general#131 · Filter by author jiangzy26 opened on Jun 17, 2026

• how to keep both the variant and invariant sites before perform analysis by popgenWindows.py

  simonhmartin/genomics_general#130 · Filter by author Yung-Chien opened on Dec 17, 2025
  1

• the subsets of pops, and the relationship among P1, P2, and P3 while using ABBABABAwindows.py

  simonhmartin/genomics_general#129 · Filter by author QianghuiZhu opened on Oct 15, 2025
  1

• GTs = [site["GTs"][name] for name in names] if extractSpecificGTs else site["GTs"] KeyError: 'ht01'

  simonhmartin/genomics_general#128 · Filter by author hm1212-ai opened on Apr 7, 2025
  1

• popgenWindows.py failing in some chromosomes

  simonhmartin/genomics_general#127 · Filter by author Agustol opened on Mar 15, 2025
  2

• How does VCF filtering and phasing influence ABBA-BABA?

  simonhmartin/genomics_general#120 · Filter by author dcmain opened on Sep 5, 2024
  2

• Pi calculation - formula for haploid data

  simonhmartin/genomics_general#119 · Filter by author OKersten opened on Aug 9, 2024
  1

• DOI?

  simonhmartin/genomics_general#116 · Filter by author kfpbennett opened on Jun 12, 2024
  2

• error transcripts codingSiteTypes

  simonhmartin/genomics_general#112 · Filter by author emgiles opened on Mar 25, 2024
  6

• Error with parseVCF.py

  simonhmartin/genomics_general#111 · Filter by author cycarthur opened on Mar 17, 2024
  1

• Query Regarding Fst Calculation Method in popgenWindows.py

  simonhmartin/genomics_general#109 · Filter by author GNWEN opened on Feb 20, 2024
  1

• ABBABABAwindows.py output halts half-way through scaffold (possibly due to outgroup?)

  simonhmartin/genomics_general#108 · Filter by author jahnringge opened on Feb 14, 2024
  2

• Can ABBA script was used with only one sample per species/population

  simonhmartin/genomics_general#104 · Filter by author jiangzy26 opened on Oct 30, 2023
  1

• ValueError: Sample B5 at Chr01:18606751 genotype . does not match explected ploidy of 2

  simonhmartin/genomics_general#99 · Filter by author ShirelyI opened on Aug 1, 2023
  4

• AssertionError: Sample ploidy (2) doesn't match number of sequences (8)

  simonhmartin/genomics_general#96 · Filter by author Ashu2195 opened on May 3, 2023
  1

• Something wrong with popgenWindows.py

  simonhmartin/genomics_general#93 · Filter by author SunJJ230120 opened on Apr 4, 2023
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• filterGenotypes.py, popgenWindows.py, popsFile "nan"

  simonhmartin/genomics_general#92 · Filter by author yangwukaidi opened on Mar 15, 2023
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• pi value of popgenWindows.py

  simonhmartin/genomics_general#88 · Filter by author KizBaolin opened on Nov 18, 2022
  1

• Possible issue with the new filterGenotypes.py

  simonhmartin/genomics_general#86 · Filter by author DaniPaulo opened on Aug 13, 2022
  1

• ValueError: invalid literal for int() with base 10: '(most'

  simonhmartin/genomics_general#85 · Filter by author ShirelyI opened on Aug 9, 2022
  3

• ValueError: dictionary update sequence element #55 has length 0; 2 is required

  simonhmartin/genomics_general#83 · Filter by author ShirelyI opened on Aug 1, 2022
  3

• ABBABABA.py encountered in double_scalars

  simonhmartin/genomics_general#81 · Filter by author Dkaaaaa opened on Jul 13, 2022
  1

• 0 results written in popgenwindows.py

  simonhmartin/genomics_general#77 · Filter by author 1661848937 opened on Jun 2, 2022
  1

• Can fd determine the direction of gene flow?

  simonhmartin/genomics_general#74 · Filter by author kuangzhuoran opened on Apr 26, 2022
  6

• p_value in ABBABABAwindows.py

  simonhmartin/genomics_general#73 · Filter by author XiaXiaTianTian opened on Apr 14, 2022
  2