ksamuk pixy issues - Githubissues

ksamuk / pixy

Software for painlessly estimating average nucleotide diversity within and between populations

https://pixy.readthedocs.io/

MIT License

113 stars 13 forks source link

issues

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

#113 AliBasuony2022 opened 4 days ago
0
'DP' FORMAT header not found

#112 pileei closed 5 days ago
2
why can't I install pixy via conda?

#111 Luo-Shigan closed 2 weeks ago
1
Pixy can't handle simple VCFs (PLINK output)

#110 somnya opened 2 weeks ago
2
Calculate Missing data per window

#109 burbrink opened 1 month ago
0
File corrupted

#108 WeixuanPlant opened 2 months ago
1
<

#107 Jesuscs049 opened 2 months ago
0
-

#106 Jesuscs049 closed 2 months ago
1
invariant vcf with ALT "*" instead of "."

#105 macurqcron opened 3 months ago
2
0 count of count_diffs and count_comparisons and all in count_missing

#104 hrluo93 opened 3 months ago
11
bug

#103 Jesuscs049 closed 2 weeks ago
0
issues about multiple alleles and phasing sites

#102 zy66-su opened 3 months ago
0
Are these filter out sites not used in the calculation?

#101 jiangzy26 opened 3 months ago
1
Using pixy without an all sites VCF?

#100 milesandersonmn opened 4 months ago
1
pixy doesnt handle masked haplotype data?

#99 jamesfifer opened 4 months ago
0
RuntimeError: VCF file is missing mandatory header line ("#CHROM...")

#98 ChenJuiYANG closed 5 months ago
4
Add support for arbitrary ploidy level (at least warn about incompatibility with polyploids)

#97 taprs opened 5 months ago
0
How to generate a allsite vcf file based on the vcf file from 1000 Genomes Project

#96 JianhuaWang95 closed 5 months ago
2
Installation issue with pixy

#95 vinod1981 closed 5 months ago
2
conda install issues with numpy and samtools

#94 seanharrington256 closed 5 months ago
1
tabix: error while loading shared libraries: libcrypto.so.1.0.0

#93 lounaDeO closed 7 months ago
5
Dxy values interpretation?

#92 MarinaSci closed 7 months ago
1
The value of Fst is negative

#91 ShirelyI closed 7 months ago
2
installation error

#90 jingydz closed 7 months ago
4
"the provided VCF appears to contain no invariant sites"

#89 MafaldaSFerreira closed 7 months ago
2
Overestimation of number differences?

#88 lisagrigoreva closed 8 months ago
1
ValueError: invalid literal for int() with base 10: ''

#87 jbruxaux closed 7 months ago
2
Error during install from conda

#86 jbruxaux closed 7 months ago
1
Provide convenient sample data in a package, such as sample data CHrX in sample scripts

#85 tongtongy666 opened 11 months 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 10 months ago
5
Version of numpy and htslib doesn't work

#82 conJUSTover closed 1 year ago
2
No variable sites

#81 avanwallendael closed 7 months ago
3
Attribute Error During Help Menu Call

#80 cizydorczyk closed 7 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 5 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
2
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
Error message - TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType

#68 aliceatikesse closed 1 year ago
1
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