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ksamuk
/
pixy
Software for painlessly estimating average nucleotide diversity within and between populations
https://pixy.readthedocs.io/
MIT License
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avg_pi was bigger than that of vcftools
#118
feiyu007
opened
5 days ago
0
Add Watterson's theta and Tajima's D into pixy
#117
npb596
opened
2 weeks ago
2
About --chromosomes option
#116
ChenJuiYANG
opened
3 weeks ago
0
can index big vcf
#115
WWz33
opened
1 month ago
0
All avg_dxy in pixy_dxy.txt is NA
#114
ala98412
opened
1 month ago
3
version 1.2.11.beta1., pixy: error: unrecognized arguments: --variant_filter_expression DP -invariant_filter_expression DP
#113
AliBasuony2022
opened
2 months ago
0
'DP' FORMAT header not found
#112
pileei
closed
2 months ago
2
why can't I install pixy via conda?
#111
Luo-Shigan
closed
2 months ago
1
Pixy can't handle simple VCFs (PLINK output)
#110
somnya
closed
4 weeks ago
2
Calculate Missing data per window
#109
burbrink
opened
3 months ago
0
File corrupted
#108
WeixuanPlant
opened
3 months ago
1
<
#107
Jesuscs049
opened
4 months ago
0
-
#106
Jesuscs049
closed
4 months ago
1
invariant vcf with ALT "*" instead of "."
#105
macurqcron
opened
4 months ago
3
0 count of count_diffs and count_comparisons and all in count_missing
#104
hrluo93
opened
4 months ago
11
bug
#103
Jesuscs049
closed
2 months ago
0
issues about multiple alleles and phasing sites
#102
zy66-su
opened
5 months ago
0
Are these filter out sites not used in the calculation?
#101
jiangzy26
opened
5 months ago
1
Using pixy without an all sites VCF?
#100
milesandersonmn
opened
5 months ago
1
pixy doesnt handle masked haplotype data?
#99
jamesfifer
opened
6 months ago
0
RuntimeError: VCF file is missing mandatory header line ("#CHROM...")
#98
ChenJuiYANG
closed
7 months ago
4
Add support for arbitrary ploidy level (at least warn about incompatibility with polyploids)
#97
taprs
opened
7 months ago
1
How to generate a allsite vcf file based on the vcf file from 1000 Genomes Project
#96
JianhuaWang95
closed
7 months ago
2
Installation issue with pixy
#95
vinod1981
closed
7 months ago
2
conda install issues with numpy and samtools
#94
seanharrington256
closed
7 months ago
1
tabix: error while loading shared libraries: libcrypto.so.1.0.0
#93
lounaDeO
closed
9 months ago
5
Dxy values interpretation?
#92
MarinaSci
closed
9 months ago
1
The value of Fst is negative
#91
ShirelyI
closed
9 months ago
2
installation error
#90
jingydz
closed
9 months ago
4
"the provided VCF appears to contain no invariant sites"
#89
MafaldaSFerreira
closed
9 months ago
2
Overestimation of number differences?
#88
lisagrigoreva
closed
10 months ago
1
ValueError: invalid literal for int() with base 10: ''
#87
jbruxaux
closed
9 months ago
2
Error during install from conda
#86
jbruxaux
closed
9 months ago
1
Provide convenient sample data in a package, such as sample data CHrX in sample scripts
#85
tongtongy666
opened
1 year ago
0
pixy (apparently) not using all requested cores
#84
rafmarcondes
closed
1 year ago
0
Why are the results so different when using pixy and vcftools
#83
Wennie-s
closed
1 year ago
5
Version of numpy and htslib doesn't work
#82
conJUSTover
closed
1 year ago
2
No variable sites
#81
avanwallendael
closed
9 months ago
3
Attribute Error During Help Menu Call
#80
cizydorczyk
closed
9 months ago
5
ability to handle sex chromosomes
#79
jtweir
opened
1 year ago
2
Support for New Missing Data Formatting from GATK
#78
ksamuk
closed
7 months ago
3
attribute error
#77
glaudelrio
closed
1 year ago
4
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
kanikaghildiyal
closed
1 year ago
4
Pixy does not detect variable sites
#75
sPuechmailleGitHub
closed
1 year ago
2
Problem running pi on pixy
#74
bvaditi
closed
1 year ago
5
IndexError: list index out of range
#73
edgarwly
closed
1 year ago
0
csi index
#72
giuliafrascarelli
opened
1 year ago
3
Pixy estimations are wrong
#71
lisagrigoreva
closed
1 year ago
2
Pandas error: too many columns specified
#70
sabrinamostoufi
closed
1 year ago
2
IndexError: list index out of range
#69
Pcariman
closed
1 year ago
2
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