Issues

• patterson_fst is algebraically identical to hudson_fst (resolves the TODO in fst.py)

  cggh/scikit-allel#456 · Filter by author isaacsight opened on Aug 20, 2026

• Clarification on size parameter in moving_garud_h (variant count vs physical bp distance)

  cggh/scikit-allel#453 · Filter by author GSYH opened on Jun 3, 2026

• Any comment on MAF filtering for XP-nSL/XP-EHH results

  cggh/scikit-allel#448 · Filter by author biozzq opened on Feb 26, 2026

• Update docs to recommend bio2zarr for VCF conversion?

  cggh/scikit-allel#437 · Filter by author jeromekelleher opened on Apr 11, 2025

• KeyError: "Unable to open object (unable to open external file, external link file name = 'xxxxxx.h5')"

  cggh/scikit-allel#413 · Filter by author yifangt-ACRD opened on Jun 14, 2024

• Question: Is allel.stats.hudson_fst() actually unbiased following Bhatia et al. 2013?

  cggh/scikit-allel#407 · Filter by author taprs opened on Feb 13, 2024
  1

• Fu and Li's D and Fay & Wu's H

  cggh/scikit-allel#392 · Filter by author crisamor opened on Mar 9, 2023

• reading data chromosome key error

  cggh/scikit-allel#387 · Filter by author snowformatics opened on Oct 5, 2022
  2

• Indexing Error for VariantTable, requires values to be monotonically increasing

  cggh/scikit-allel#384 · Filter by author npb596 opened on Jul 23, 2022

• Behaviour of count_alleles() when all genotypes are missing

  cggh/scikit-allel#379 · Filter by author alimanfoo opened on Apr 13, 2022

• Copying GenotypeDaskArray returns DaskArray

  cggh/scikit-allel#377 · Filter by author travc opened on Mar 10, 2022

• allel.read_vcf RuntimeError: VCF file is missing mandatory header line ("#CHROM...")

  cggh/scikit-allel#376 · Filter by author nathanvranken opened on Feb 16, 2022
  3

• Feature Request - unphased IHS/XPEHH

  cggh/scikit-allel#374 · Filter by author kullrich opened on Jan 21, 2022
  1

• error results from allel.pbs

  cggh/scikit-allel#372 · Filter by author sandyplus opened on Dec 2, 2021

• Haplotype data

  cggh/scikit-allel#367 · Filter by author pengyan19 opened on Aug 25, 2021

• windowing: weird(?) behavior with the last window

  cggh/scikit-allel#363 · Filter by author mufernando opened on Jun 25, 2021
  4

• FILTER_PASS when FILTER has '.'

  cggh/scikit-allel#359 · Filter by author joshfactorial opened on Apr 20, 2021

• Calculating the sequence diversity between two variants returns a key error

  cggh/scikit-allel#356 · Filter by author vsbuffalo opened on Mar 13, 2021

• How to use query atrr of array

  cggh/scikit-allel#355 · Filter by author KazegamiKuon opened on Mar 13, 2021

• Unable to open object (object 'pcontig_000' doesn't exist)

  cggh/scikit-allel#351 · Filter by author Ram-Nagar opened on Feb 11, 2021

• ALT fields with . + seq in vcf_to_dataframe are annotated as nan.

  cggh/scikit-allel#349 · Filter by author gmgs-999 opened on Jan 29, 2021

• Exporting genotype to a file

  cggh/scikit-allel#348 · Filter by author vappiah opened on Jan 27, 2021
  3

• optional dependency on bcolz

  cggh/scikit-allel#345 · Filter by author Anthchirp opened on Nov 2, 2020
  1

• draw LD heatmap?

  cggh/scikit-allel#343 · Filter by author shenweima opened on Oct 22, 2020

• Negative GQ values after vcf_to_hdf5

  cggh/scikit-allel#341 · Filter by author grlewis333 opened on Sep 22, 2020
  3