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seppinho
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haplogrep-cmd
HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.
https://haplogrep.i-med.ac.at/
MIT License
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Phylotree
#52
rohandavidg
opened
1 year ago
0
Enhancement: Calculate Mutation Burden
#51
DarioS
opened
1 year ago
0
Errors if Whole Genome VCF Input
#50
DarioS
opened
1 year ago
0
--rsrs option crashes
#49
JoshuaDanielRubin
opened
2 years ago
4
how get the sample quality and HG quality using command line haplogrep
#48
rarahmati
opened
2 years ago
0
java.nio.file.DirectoryNotEmptyException
#47
WZo0o
closed
1 year ago
2
Return correct exit code
#46
lukfor
closed
3 years ago
1
Haplogrep error with a vcf-merge file.
#45
VGDEC
opened
3 years ago
1
Update code formatting
#44
lukfor
closed
3 years ago
1
can't install haplogrep-cmd
#43
kopelol
closed
3 years ago
5
haplogrep on non-human species
#42
leleory
opened
3 years ago
1
Installation not working
#41
divonlan
closed
3 years ago
1
Issues with processing indels in VCF
#40
shadrinams
opened
3 years ago
1
Bug #38 Add tarLongFileMode to pom.xml to allow big user IDs
#39
david-ma
closed
3 years ago
2
Bug: Fails to build when user ID is too big. Add tarLongFileMode to pom.xml
#38
david-ma
closed
3 years ago
1
Quality ∞% ?
#37
Alessio0796
opened
3 years ago
4
add fasta export for console version
#36
haansi
closed
3 years ago
1
Haplogroup Quality score >1?
#35
nanshanjin
opened
4 years ago
5
input file error on 2.2.0
#34
jamigo
closed
4 years ago
4
Remove jbwa-xxxx folder after running HaploGrep
#33
alexhbnr
closed
4 years ago
4
Microarrays and missing data, `--chip`
#32
stephenturner
opened
4 years ago
0
Feature request: least common ancestor for equally scoring haplogroups
#31
stephenturner
opened
4 years ago
4
MicroArrays and back-mutations
#30
haansi
opened
4 years ago
0
Is the XML file mal-formatted?
#29
mocksu
closed
5 years ago
12
Error on output on 'Not Found' variants
#28
nuin
closed
5 years ago
1
Export FASTA using the command line version
#27
teepean
opened
5 years ago
1
Heteroplasmic insertion
#26
haansi
closed
5 years ago
1
Add alignment rules to place indels correctly
#25
seppinho
closed
5 years ago
1
Bug on running haplogrep on windows
#24
elffuos
closed
5 years ago
2
pom.xml warning: jdom is written twice and doesn't correspond to dependency org.jdom:jdom:*:*
#23
monkollek
closed
5 years ago
0
pom.xml error. incorrect paths for resources: phylotree, weights and annotation
#22
monkollek
closed
5 years ago
0
Running HaploGrep v2.1.18on MacOS
#21
elffuos
closed
5 years ago
1
Allow FastA file extension other than "fasta"?
#20
alexhbnr
closed
5 years ago
1
bump version number
#19
stephenturner
closed
5 years ago
0
Fix MacOS issue for FASTA
#18
seppinho
closed
5 years ago
15
Add Contamination Simulator
#17
haansi
closed
5 years ago
1
FASTA failure - missing file
#16
sushilashenoy
closed
5 years ago
6
Add test-cases for RSRS
#15
haansi
opened
5 years ago
0
Feature fasta
#14
seppinho
closed
5 years ago
0
Add recombination feature in console version
#13
haansi
closed
3 years ago
0
Allow export of first-n best haplogroups
#12
haansi
closed
5 years ago
7
Extra space on columns when --extend-report is used
#11
nuin
closed
6 years ago
0
Error when using --lineage option
#10
nuin
closed
5 years ago
13
Start Classification... java.lang.NumberFormatException: For input string: "15940*"
#9
snashraf
closed
6 years ago
8
Error message for non-haploid genotypes in vcf
#8
haansi
closed
6 years ago
0
Provide a Haplogrep RSRS Version
#7
seppinho
closed
6 years ago
2
Annotate FASTA file
#6
nuin
closed
6 years ago
4
Error - cannot find input file haplogrep 2.1.8
#5
jayaramanp
closed
6 years ago
0
Recheck backmutations in remaining polymorphisms
#4
haansi
opened
6 years ago
0
Support Fasta
#3
seppinho
closed
5 years ago
0
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