ksamuk/pixy

Issues

• Should sites with no depth coverage by included or excluded from VCF files while using Whole genome data for Dxy calculation?

  #119 opened a month ago by vincianem
  0

• Support for New Missing Data Formatting from GATK

  #78 opened 9 months ago by ksamuk
  4

• All avg_dxy in pixy_dxy.txt is NA

  #114 opened 4 months ago by ala98412
  3

• avg_pi was bigger than that of vcftools

  #118 opened 2 months ago by feiyu007
  0

• About --chromosomes option

  #116 opened 3 months ago by ChenJuiYANG
  0

• invariant vcf with ALT "*" instead of "."

  #105 opened 7 months ago by macurqcron
  3

• Pixy can't handle simple VCFs (PLINK output)

  #110 opened 3 months ago by somnya
  2

• can index big vcf

  #115 opened 3 months ago by WWz33
  0

• csi index

  #72 opened 2 years ago by giuliafrascarelli
  3

• Add support for arbitrary ploidy level (at least warn about incompatibility with polyploids)

  #97 opened 10 months ago by taprs
  1

• version 1.2.11.beta1., pixy: error: unrecognized arguments: --variant_filter_expression DP -invariant_filter_expression DP

  #113 opened 4 months ago by AliBasuony2022
  0

• 'DP' FORMAT header not found

  #112 opened 4 months ago by pileei
  2

• 0 count of count_diffs and count_comparisons and all in count_missing

  #104 opened 7 months ago by hrluo93
  11

• why can't I install pixy via conda?

  #111 opened 5 months ago by Luo-Shigan
  1

• bug

  #103 opened 5 months ago by Jesuscs049
  0

• Calculate Missing data per window

  #109 opened 5 months ago by burbrink
  0

• File corrupted

  #108 opened 6 months ago by WeixuanPlant
  1

• <

  #107 opened 7 months ago by Jesuscs049
  0

• -

  #106 opened 7 months ago by Jesuscs049
  1

• Are these filter out sites not used in the calculation?

  #101 opened 8 months ago by jiangzy26
  1

• issues about multiple alleles and phasing sites

  #102 opened 7 months ago by zy66-su
  0

• Using pixy without an all sites VCF?

  #100 opened 8 months ago by milesandersonmn
  1

• pixy doesnt handle masked haplotype data?

  #99 opened 9 months ago by jamesfifer
  0

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

  #98 opened 10 months ago by ChenJuiYANG
  4

• Installation issue with pixy

  #95 opened 10 months ago by vinod1981
  2

• How to generate a allsite vcf file based on the vcf file from 1000 Genomes Project

  #96 opened 10 months ago by JianhuaWang95
  2

• conda install issues with numpy and samtools

  #94 opened 10 months ago by seanharrington256
  1

• No variable sites

  #81 opened a year ago by avanwallendael
  3

• ability to handle sex chromosomes

  #79 opened 2 years ago by jtweir
  2

• tabix: error while loading shared libraries: libcrypto.so.1.0.0

  #93 opened a year ago by lounaDeO
  5

• Dxy values interpretation?

  #92 opened a year ago by MarinaSci
  1

• Attribute Error During Help Menu Call

  #80 opened a year ago by cizydorczyk
  5

• Error during install from conda

  #86 opened a year ago by jbruxaux
  1

• installation error

  #90 opened a year ago by jingydz
  4

• "the provided VCF appears to contain no invariant sites"

  #89 opened a year ago by MafaldaSFerreira
  2

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

  #87 opened a year ago by jbruxaux
  2

• The value of Fst is negative

  #91 opened a year ago by ShirelyI
  2

• Overestimation of number differences?

  #88 opened a year ago by lisagrigoreva
  1

• Provide convenient sample data in a package, such as sample data CHrX in sample scripts

  #85 opened a year ago by tongtongy666
  0

• Why are the results so different when using pixy and vcftools

  #83 opened a year ago by Wennie-s
  5

• pixy (apparently) not using all requested cores

  #84 opened a year ago by rafmarcondes
  0

• Hello, While running the pixy software after converting vcf file with invariant sites using bcftools, I am getting the following error:UnicodeDecodeError: 'utf-8' codec cant decode byte 0x8b in position 1: invalid start byte; Could you please help me to resolve this error?

  #76 opened 2 years ago by kanikaghildiyal
  4

• Version of numpy and htslib doesn't work

  #82 opened a year ago by conJUSTover
  2

• attribute error

  #77 opened 2 years ago by glaudelrio
  4

• Problem running pi on pixy

  #74 opened 2 years ago by bvaditi
  5

• Pixy does not detect variable sites

  #75 opened 2 years ago by sPuechmailleGitHub
  2

• IndexError: list index out of range

  #73 opened 2 years ago by edgarwly
  0

• Pixy estimations are wrong

  #71 opened 2 years ago by lisagrigoreva
  2

• IndexError: list index out of range

  #69 opened 2 years ago by Pcariman
  2

• Pandas error: too many columns specified

  #70 opened 2 years ago by sabrinamostoufi
  2