simonhmartin genomics_general issues

simonhmartin / genomics_general

General tools for genomic analyses.

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calculate dxy and ABBA,do the input files need to provide invariant sites?

#122 chelisa opened 3 weeks ago
0
Error while parsing VCF

#121 vincianem closed 1 month ago
0
How does VCF filtering and phasing influence ABBA-BABA?

#120 dcmain opened 2 months ago
2
Pi calculation - formula for haploid data

#119 OKersten opened 3 months ago
1
Why is the output matrix of distMat.py not a diagonal zero matrix?

#118 NCtraveling closed 3 months ago
1
error with popgenWindows.py

#117 Gefsy closed 4 months ago
0
DOI?

#116 kfpbennett opened 5 months ago
1
phased

#115 chen1238 closed 6 months ago
3
--minSites set

#114 hrluo93 closed 7 months ago
1
parseVCF.py bug?

#113 angusdavison closed 6 months ago
1
error transcripts codingSiteTypes

#112 emgiles opened 8 months ago
6
Error with parseVCF.py

#111 cycarthur opened 8 months ago
1
popgenWindows only runs on some scaffolds

#110 emgiles closed 8 months ago
4
Query Regarding Fst Calculation Method in popgenWindows.py

#109 weirdfanny opened 9 months ago
1
ABBABABAwindows.py output halts half-way through scaffold (possibly due to outgroup?)

#108 jahnringge opened 9 months ago
2
error with popgenWindows.py: "All populations must be represented by at least one sample."

#107 mayjean21 closed 1 year ago
2
IndexError: list index out of range - freq & sfs

#106 yzliu01 closed 9 months ago
2
ABBABABAwindows.py "TypeError: slidingCoordWindows()"

#105 ljchueca closed 1 year ago
2
Can ABBA script was used with only one sample per species/population

#104 jiangzy26 opened 1 year ago
1
problem with phyml_sliding_windows.py

#103 InfiniteLaugh closed 8 months ago
6
Scaffold warning

#102 swift-213 closed 1 year ago
0
In the results of popgenWindows.py, Dxy > Fst

#101 yangwukaidi closed 1 year ago
2
filterGenotypes does not accept 'randomAlleles' as an output format

#100 dcmain closed 1 year ago
6
ValueError: Sample B5 at Chr01:18606751 genotype . does not match explected ploidy of 2

#99 ShirelyI opened 1 year ago
4
How to cite ？

#98 zy66-su closed 1 year ago
2
popgenWindows.py Dxy estimates are large with vcf with invariant sites

#97 MatteoSebastianelli closed 1 year ago
7
AssertionError: Sample ploidy (2) doesn't match number of sequences (8)

#96 Ashu2195 opened 1 year ago
1
Some bugs in popgenWindows.py

#95 wushyer closed 1 year ago
5
Empty outfile from popgenWindow.py

#94 HZAUzyz closed 1 year ago
0
Something wrong with popgenWindows.py

#93 SunJJ230120 opened 1 year ago
1
filterGenotypes.py, popgenWindows.py, popsFile "nan"

#92 yangwukaidi opened 1 year ago
1
raxml_sliding_windows.py：：Unable to identify outgroups

#91 cheninouc closed 1 year ago
2
ValueError: Sample NR112 at Scaffold_1:1 genotype ./././. does not match explected ploidy of 2

#90 wangjie07070910 closed 1 year ago
7
parseVCF.py error

#89 EmilyPhelps closed 1 year ago
3
pi value of popgenWindows.py

#88 KizBaolin opened 2 years ago
1
pi value is large

#87 chen1238 closed 2 years ago
10
Possible issue with the new filterGenotypes.py

#86 DaniPaulo opened 2 years ago
1
ValueError: invalid literal for int() with base 10: '(most'

#85 ShirelyI opened 2 years ago
3
something goes wrong when used "raxml_sliding_windows.py"

#84 zhangqiong151 closed 1 year ago
2
ValueError: dictionary update sequence element #55 has length 0; 2 is required

#83 ShirelyI opened 2 years ago
3
significance of Fd for sliding windows

#82 stubbsrl closed 2 years ago
2
ABBABABA.py encountered in double_scalars

#81 Dkaaaaa opened 2 years ago
1
ABBABABAwindows.py error

#80 rturba closed 2 years ago
4
popgenWindows.py output skips some chromosomes

#79 rturba closed 2 years ago
1
IndexError in raxml_sliding_window.py

#78 MinaEvo closed 2 years ago
2
0 results written in popgenwindows.py

#77 1661848937 opened 2 years ago
1
Error in jackknife procedure

#76 DuttaAnik closed 2 years ago
2
Error message in popgenWindows.py

#75 DuttaAnik closed 2 years ago
7
Can fd determine the direction of gene flow?

#74 kuangzhuoran opened 2 years ago
6
p_value in ABBABABAwindows.py

#73 XiaXiaTianTian opened 2 years ago
2