seppinho/haplogrep-cmd

Issues

• Phylotree

  #52 opened 2 years ago by rohandavidg
  0

• Enhancement: Calculate Mutation Burden

  #51 opened 2 years ago by DarioS
  0

• Errors if Whole Genome VCF Input

  #50 opened 2 years ago by DarioS
  0

• --rsrs option crashes

  #49 opened 3 years ago by JoshuaDanielRubin
  4

• java.nio.file.DirectoryNotEmptyException

  #47 opened 2 years ago by WZo0o
  2

• how get the sample quality and HG quality using command line haplogrep

  #48 opened 3 years ago by rarahmati
  0

• Add recombination feature in console version

  #13 opened 3 years ago by haansi
  0

• Haplogrep error with a vcf-merge file.

  #45 opened 3 years ago by VGDEC
  1

• Quality ∞% ?

  #37 opened 4 years ago by Alessio0796
  4

• Issues with processing indels in VCF

  #40 opened 4 years ago by shadrinams
  1

• haplogrep on non-human species

  #42 opened 4 years ago by leleory
  1

• Bug: Fails to build when user ID is too big. Add tarLongFileMode to pom.xml

  #38 opened 3 years ago by david-ma
  1

• Installation not working

  #41 opened 3 years ago by divonlan
  1

• can't install haplogrep-cmd

  #43 opened 3 years ago by kopelol
  5

• Haplogroup Quality score >1？

  #35 opened 4 years ago by nanshanjin
  5

• Feature request: least common ancestor for equally scoring haplogroups

  #31 opened 5 years ago by stephenturner
  4

• Remove jbwa-xxxx folder after running HaploGrep

  #33 opened 5 years ago by alexhbnr
  4

• input file error on 2.2.0

  #34 opened 5 years ago by jamigo
  4

• Microarrays and missing data, `--chip`

  #32 opened 5 years ago by stephenturner
  0

• MicroArrays and back-mutations

  #30 opened 5 years ago by haansi
  0

• Is the XML file mal-formatted?

  #29 opened 5 years ago by mocksu
  12

• Heteroplasmic insertion

  #26 opened 5 years ago by haansi
  1

• Add Contamination Simulator

  #17 opened 5 years ago by haansi
  1

• Bug on running haplogrep on windows

  #24 opened 5 years ago by elffuos
  2

• Add alignment rules to place indels correctly

  #25 opened 5 years ago by seppinho
  1

• Error on output on 'Not Found' variants

  #28 opened 5 years ago by nuin
  1

• Export FASTA using the command line version

  #27 opened 6 years ago by teepean
  1

• Fix MacOS issue for FASTA

  #18 opened 6 years ago by seppinho
  15

• pom.xml error. incorrect paths for resources: phylotree, weights and annotation

  #22 opened 6 years ago by monkollek
  0

• pom.xml warning: jdom is written twice and doesn't correspond to dependency org.jdom:jdom:*:*

  #23 opened 6 years ago by monkollek
  0

• Running HaploGrep v2.1.18on MacOS

  #21 opened 6 years ago by elffuos
  1

• Allow FastA file extension other than "fasta"?

  #20 opened 6 years ago by alexhbnr
  1

• Error when using --lineage option

  #10 opened 6 years ago by nuin
  13

• Allow export of first-n best haplogroups

  #12 opened 6 years ago by haansi
  7

• Recheck backmutations in remaining polymorphisms

  #4 opened 6 years ago by haansi
  0

• Add test-cases for RSRS

  #15 opened 6 years ago by haansi
  0

• FASTA failure - missing file

  #16 opened 6 years ago by sushilashenoy
  6

• Support Fasta

  #3 opened 6 years ago by seppinho
  0

• Start Classification... java.lang.NumberFormatException: For input string: "15940*"

  #9 opened 6 years ago by snashraf
  8

• Extra space on columns when --extend-report is used

  #11 opened 6 years ago by nuin
  0

• Error message for non-haploid genotypes in vcf

  #8 opened 6 years ago by haansi
  0

• Provide a Haplogrep RSRS Version

  #7 opened 6 years ago by seppinho
  2

• Annotate FASTA file

  #6 opened 6 years ago by nuin
  4

• Error - cannot find input file haplogrep 2.1.8

  #5 opened 6 years ago by jayaramanp
  0

• Support VCF input format

  #2 opened 6 years ago by seppinho
  0

• Distance metric as parameter

  #1 opened 7 years ago by haansi
  1