FRED-2/OptiType

Issues

• Mouse WES

  #150 opened 2 months ago by dincerkilic
  0

• Ways to update hla reference/allele data?

  #112 opened 4 years ago by ikarus97
  7

• OptiType Fails to Open Intermediate BAM File

  #149 opened 3 months ago by valeriaMCuevas
  0

• IOError: [Errno 2] could not open alignment file

  #148 opened 4 months ago by lukaas33
  0

• IOError: [Errno 2] could not open alignment file `result/2020_07_08_14_33_58/2020_07_08_14_33_58_1.bam`: No such file or directory

  #110 opened 4 years ago by frankligy
  6

• The SolverFactory was unable to create the solver "glpk"

  #128 opened 5 months ago by iskysinger
  1

• Does OptiType only predict alleles in "freq_alleles"

  #134 opened 5 months ago by mourisl
  1

• this team is no longer maintained

  #140 opened a year ago by SunYong0821
  1

• Running OptiType for non human samples

  #97 opened 5 months ago by drtamermansour
  6

• Is it based on hg38 genome?

  #135 opened 5 months ago by xiasijian
  3

• unpaired reads, no mismatches, ambiguous

  #142 opened 5 months ago by QianRongAn
  1

• core dumped bad_alloc in seqan

  #145 opened 5 months ago by vodkatad
  6

• Hi dear @andras86 , What's the meanning for "introns from " as picture beblow? I found it apprearing in https://github.com/FRED-2/OptiType/blob/master/hlatyper.py

  #133 opened 5 months ago by whiffen-cann
  1

• Installation problem with pyomo module

  #139 opened 5 months ago by Elisa89m
  1

• Bam file to prefilter reads

  #147 opened 5 months ago by SirKuikka
  1

• OptiType killed OOM

  #120 opened 4 years ago by Akazhiel
  4

• could not open alignment file

  #130 opened 9 months ago by tamlav
  4

• Want to use Optitype HLA results as input file for pVACseq, if someone could provide suggestion?

  #138 opened 9 months ago by edceeyuchen
  2

• Issue with downloading OptiType docker image

  #144 opened 9 months ago by mwu2001
  1

• Razers3 being slow

  #143 opened a year ago by SirKuikka
  1

• HLA typing 10x scRNA-seq data with Optitype

  #141 opened a year ago by Githubuser3838
  0

• AttributeError: 'Index' object has no attribute 'difference'

  #115 opened 4 years ago by renyuan01
  2

• Maximal read length of 0 bps exceeded

  #137 opened 2 years ago by frankligy
  0

• ValueError: too many values to unpack

  #136 opened 2 years ago by szabolcstarapcsak
  0

• what about MICA MICB typing

  #127 opened 3 years ago by dingying85
  1

• error using docker

  #132 opened 2 years ago by anoronh4
  0

• output file column description

  #131 opened 2 years ago by cjieming2
  0

• OptiType returns ValueError with some samples while running just fine with others

  #129 opened 3 years ago by isinaltinkaya
  0

• conda installation issue

  #124 opened 3 years ago by OrielResearchCure
  1

• Optitype memory error in v1.3.5 due to pandas' reindex

  #125 opened 3 years ago by jnktsj
  3

• Optitype fails to run silently and does not generate the resulting TSV file

  #126 opened 3 years ago by b-niu
  0

• conda installation issue

  #123 opened 3 years ago by OrielResearchCure
  0

• IOError: [Errno 2] could not open alignment file

  #116 opened 4 years ago by dstueckm
  6

• HLA class II prediction

  #107 opened 5 years ago by PKazakova
  5

• RAM fully occupied with very small input fastq

  #122 opened 3 years ago by zyh4482
  0

• Updated Docker version

  #121 opened 4 years ago by YingYa
  0

• Commands for Singularity Bootstrap of Docker Image

  #114 opened 4 years ago by ilovesquishy
  1

• h:363 FAILED! (Uncaught exception of type seqan::UnexpectedEnd: Unexpected end of input.)

  #118 opened 4 years ago by jingydz
  5

• OptiType mapping memory issues

  #93 opened 5 years ago by geejaytee
  1

• How to deal with tumor-only samples?

  #119 opened 4 years ago by qindan2008
  0

• Read counts for each HLA allele

  #113 opened 4 years ago by dpwickland
  0

• Error with solver

  #111 opened 4 years ago by warrenlr
  1

• "ValueError: Length mismatch"

  #109 opened 4 years ago by GBeattie
  0

• OptiType crashes after loading reads

  #100 opened 5 years ago by TimFugmann
  4

• Optitype crashes with python2.7.17 due to configparser

  #101 opened 5 years ago by naumenko-sa
  2

• OptiType crash due to pandas deprecation

  #102 opened 5 years ago by Stikus
  1

• How to output the result with 8 digits ?

  #95 opened 5 years ago by lidd77
  1

• Downloading MNIST dataset

  #98 opened 5 years ago by prachikashikar
  0

• Does OptiType care about read groups?

  #96 opened 5 years ago by Stikus
  9

• Whether Optitype supports the target sequencing data ?

  #94 opened 5 years ago by lidd77
  0