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harrispopgen
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mutyper
Ancestral k-mer mutation types for SNP data
https://harrispopgen.github.io/mutyper/
MIT License
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New GATK missing genotype annotation
#50
WSDeWitt
opened
5 months ago
0
JOSS citation
#49
WSDeWitt
closed
1 year ago
0
JOSS requested affiliation edits
#48
WSDeWitt
closed
1 year ago
0
JOSS review
#47
WSDeWitt
closed
1 year ago
0
Example usage: reduce assumptions
#46
izabelcavassim
closed
1 year ago
0
Add State of the field
#45
izabelcavassim
closed
1 year ago
1
Add Community Guidelines
#44
izabelcavassim
closed
1 year ago
2
Fix Documentation link
#43
izabelcavassim
closed
1 year ago
0
Fix references in https://github.com/harrispopgen/mutyper/blob/master/paper/paper.md
#42
izabelcavassim
closed
1 year ago
3
Integration with Hail
#41
vladsavelyev
opened
1 year ago
1
JOSS prereview
#40
WSDeWitt
closed
1 year ago
1
JOSS paper
#39
WSDeWitt
closed
1 year ago
2
numpy implementation for spectra
#38
Lukez-pi
closed
1 year ago
1
issue 36: dealing with missing genotypes with mutyper variants
#37
Lukez-pi
closed
1 year ago
0
mutyper variants converts missing genotypes to 0
#36
Lukez-pi
closed
1 year ago
0
Changed the 'number' type of 'mutation type' to A in the VCF header
#35
Lukez-pi
closed
2 years ago
3
Don't count `phase==True` toward genotypes
#34
WSDeWitt
closed
2 years ago
0
CLI tests
#33
WSDeWitt
closed
2 years ago
0
Move docs build from the default branch to a orphan branch, and workflow to build on push to master
#32
WSDeWitt
closed
2 years ago
0
Added a fix for adding too many counts when the GT is unknown
#31
mrvollger
closed
2 years ago
0
more mutyper counts in spectra than expected
#30
mrvollger
closed
2 years ago
13
Docstweaks
#29
WSDeWitt
closed
2 years ago
0
Fix for ancestral subcommand compressed fasta input, extra logging info, and a snakemake
#28
mrvollger
closed
2 years ago
1
Issue with directionality of the chain file and possible fasta indexing bug.
#27
mrvollger
closed
2 years ago
3
mutyper targets can't handle compressed bed files
#26
ab08028
opened
3 years ago
0
14 strandedness test
#25
WSDeWitt
closed
3 years ago
0
Proposed fix to bug #14
#24
RenzoTale88
closed
3 years ago
0
Fix bug #20
#23
RenzoTale88
closed
3 years ago
1
spectra for haploids
#22
WSDeWitt
closed
3 years ago
0
haploid counting in mutyper spectra
#21
ab08028
closed
3 years ago
6
Problem with ancestor command
#20
RenzoTale88
closed
3 years ago
6
haploid VCF parsing
#19
WSDeWitt
closed
3 years ago
0
polarize genotypes, closes #17
#18
WSDeWitt
closed
3 years ago
1
ancestral polarization of individual genotypes
#17
WSDeWitt
closed
3 years ago
0
Randomize feature for spectra
#16
goldmich
closed
3 years ago
1
kSFS
#15
barlavi1
closed
3 years ago
1
Strandedness issue
#14
RenzoTale88
closed
3 years ago
5
4 chains parse
#13
WSDeWitt
closed
3 years ago
0
Handle missing genotypes in input VCFs with hypergeometric projection for ksfs
#12
WSDeWitt
opened
3 years ago
0
performance issues with accessing bgzipped ancestral fastas
#11
WSDeWitt
opened
3 years ago
3
Population spectra
#10
WSDeWitt
closed
4 years ago
0
strand-aware mutation contexts
#9
WSDeWitt
closed
4 years ago
0
population mutation spectra?
#8
goldmich
closed
4 years ago
2
might need to include the gcc package dependency in setup.py
#7
Lukez-pi
closed
4 years ago
1
use strand_file BED argument to orient context instead of collapsing by revcomp
#6
WSDeWitt
closed
4 years ago
1
spectra methods for Python API (not just CLI)
#5
WSDeWitt
opened
4 years ago
0
ancestral genome estimation
#4
WSDeWitt
closed
3 years ago
1
Create LICENSE
#3
WSDeWitt
closed
4 years ago
0
packagify
#2
WSDeWitt
closed
4 years ago
0
docs
#1
WSDeWitt
closed
4 years ago
0
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