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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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IndexError: list index out of range
#67
jiangqiuqiuu
closed
1 year ago
4
What has been calculated in the pi output if there is only one individual?
#66
Jolleboll
closed
1 year ago
4
can pixy be used in haploid species
#65
wushyer
closed
1 year ago
3
VCF from fast file?
#64
olgakozhar
closed
1 year ago
2
Better Error Message for .tbi Files in Place of VCFs
#63
ksamuk
opened
2 years ago
0
UnicodeDecodeError when running pixy for the first time
#62
olgakozhar
closed
2 years ago
4
heterozygous sites increase nucleotide diversity?
#61
caixu0518
closed
2 years ago
1
[pixy] ERROR: the provided VCF appears to contain no variable sites.
#60
StefanoLonardi
closed
2 years ago
2
Understanding how missing data are taken into account in avg_pi
#59
gsgarlata
closed
2 years ago
4
Hard or soft filtering input VCF?
#58
mwersebe
closed
2 years ago
2
Per marker stats
#57
ricebrian
closed
2 years ago
2
window_size 1
#56
fxfish
closed
2 years ago
1
--sites_file argument ouputs only NAs in avg_pi column
#55
tshalev
closed
2 years ago
10
Output Fst variance components
#54
SethMusker
opened
2 years ago
0
permutation test
#53
biozzq
closed
1 year ago
1
Make Pixy into a library for importing into Python scripts
#52
vlrieg
closed
2 years ago
2
average fst across windows
#51
danielwood1992
closed
2 years ago
4
window and step options
#50
amsamani
closed
2 years ago
1
LD pruning before calculating Fst/dxy?
#49
nitinra
closed
2 years ago
2
sites_file argument not working
#48
JesseGarcia562
closed
2 years ago
5
Haploid VCF
#47
Jolvii85
closed
2 years ago
2
Duplicated sites in pixy output using bed intervals?
#46
jsalt
closed
2 years ago
3
pi output gives NA values when there is viable data
#45
anitato
closed
2 years ago
5
error says my vcf has no invariant
#44
amsamani
closed
2 years ago
9
Best practice for estimating πN/πS in pixy
#43
tshalev
closed
2 years ago
2
Fst estimation error
#42
Gandasegui
closed
2 years ago
10
How should I compare my pi results from pixy with studies that use other approaches?
#41
tshalev
closed
2 years ago
2
Single site calculation of dxy
#40
BaHole
closed
3 years ago
3
CHROMOSOMES
#39
BaHole
closed
3 years ago
1
Tajima's D
#38
vlrieg
opened
3 years ago
4
Filtering on site quality removes many invariant sites in a VCF from GATK
#37
davidecarlson
closed
3 years ago
8
Persite Fst - 'float' object is not iterable
#36
erikenbody
closed
3 years ago
7
Fix setup.py for pip install
#35
niemasd
closed
3 years ago
0
Installing pixy using "pip install pixy" doesn't yield "pixy" executable
#34
niemasd
closed
3 years ago
3
chromosome and zarr_path
#33
BaHole
closed
3 years ago
4
bed file regions (with chromosomes just as numbers)
#32
danielwood1992
closed
3 years ago
2
KeyError: nan
#31
djeffares
closed
3 years ago
11
Hudson FST
#30
biozzq
closed
3 years ago
1
--output_folder prepends working directory path onto paths from root
#29
tintori
closed
3 years ago
1
No invariant sites found in simulated VCF file
#28
vlrieg
closed
3 years ago
5
vcf file indexing error
#27
sandipmkale
closed
3 years ago
3
Pi calculation error - ValueError: Cannot convert non-finite values (NA or inf) to integer
#26
mishaploid
closed
3 years ago
4
TypeError: zip argument #3
#25
ClaudimarceO
closed
3 years ago
2
Missing comma in requirements for setup.py
#24
mishaploid
closed
3 years ago
1
Issue in D xy calculation
#23
Doniol-Valcroze
closed
3 years ago
3
bed file as input
#22
stsmall
closed
3 years ago
2
IndexError during Fst calc when chrom has no variants passing filter
#21
mscharmann
closed
3 years ago
2
import pixy
#20
MAl-Ajaji
closed
3 years ago
1
add option to always have intervals spanning entire chromosomes
#19
mscharmann
closed
3 years ago
4
Error in NUMEXPR dependency
#18
mscharmann
closed
3 years ago
3
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