Illumina/hap.py

Issues

• query region doesn't contain variants

  #197 opened a month ago by alisamatisse
  1

• VAF considered by HAPPY sensitivity and specificity

  #198 opened a month ago by Belle-AM
  0

• Call for the TRUTH_VCF file

  #196 opened a month ago by thangnx1012
  0

• CMake Error at CMakeLists.txt:32 (message): Building external dependencies has failed

  #171 opened 2 years ago by oranges7
  1

• Preoprocess might fail when complex SVs are presented

  #195 opened a month ago by LYC-vio
  0

• Misclassification of FP as TP

  #194 opened 3 months ago by sainsachiko
  0

• som.py throws error `cannot call `vectorize` on size 0 inputs unless `otypes` is set`

  #193 opened 4 months ago by marrip
  0

• Parsing results VCF gives different counts of TRUTH FN than summary

  #170 opened 2 years ago by BrianLohman
  2

• Persistent Warning Regarding INFO/IMPORT_FAIL in VCF Header

  #192 opened 6 months ago by Iredcg
  1

• Docker build failed

  #186 opened a year ago by MAlwaz
  1

• TRUTH.TOTAL differs despite having used the same TRUTH SET

  #165 opened 2 years ago by robertzeibich
  3

• Using --usefiltered-truth results in incorrect FP calls for filtered variants in the truth (xcmp)

  #191 opened 8 months ago by melferink
  0

• Make a new pre-built docker image?

  #190 opened 8 months ago by Luobiny
  0

• While using hap.py, there is a problem:

  #189 opened 9 months ago by pioneer-pi
  0

• Can't find reference

  #188 opened 10 months ago by ktruve
  1

• [E::bgzf_uncompress] inflate failed: invalid distance too far back

  #185 opened a year ago by liukeweiaway
  1

• How is the false positive rate calculated in som.py stats?

  #187 opened a year ago by Krannich479
  0

• ROC and PR curve

  #179 opened 2 years ago by ESDeutekom
  2

• running into build error with CMake

  #166 opened 2 years ago by Overcraft90
  3

• WES TI TV ratio

  #167 opened a year ago by solivehong
  2

• Link provide in email is broken

  #182 opened 2 years ago by Manuel-DominguezCBG
  1

• VCF format issues with --write-vcf, - FORMAT field inconsistencies

  #175 opened 2 years ago by insilicool
  1

• Handle duplicated lines in normalized .vcf file

  #160 opened 2 years ago by YuanfengZhang
  3

• Incorrect number of FORMAT/AD values on scmp-distance engine

  #181 opened 2 years ago by jerrywongzy
  0

• Docker fails to build for both bases

  #180 opened 2 years ago by rickymagner
  0

• Calculation of METRIC.Precision

  #157 opened 3 years ago by b-math
  1

• Hap.py not working with singularity

  #164 opened 3 years ago by NoamYakar23
  1

• Docker Implementation: Several Error Messages Related to "preprocess"

  #178 opened 2 years ago by cwarden45
  1

• error code 1

  #177 opened 2 years ago by NRusca
  0

• Trying to print sequence when we mean contig name

  #176 opened 2 years ago by adamnovak
  0

• missing reference

  #174 opened 2 years ago by Overcraft90
  1

• Integrating vcfdist as a comparison engine into hap.py

  #173 opened 2 years ago by TimD1
  0

• Error running BCFTOOLS :Argument list too long

  #172 opened 2 years ago by zhaolx01
  0

• segmentation fault at gvcf2bed

  #154 opened 3 years ago by meredith705
  7

• pre.py -> vcfcheck fails due to call with invalid genotype (non-existent allele)

  #169 opened 2 years ago by robertzeibich
  0

• Confused with the interpretation when having TRUTH.FN and QUERY.FP

  #168 opened 2 years ago by Manuel-DominguezCBG
  2

• problems about default and customized ref.fasta in variant normalisation process

  #159 opened 3 years ago by YuanfengZhang
  1

• PreProcessing creates un-ordered VCF

  #163 opened 3 years ago by MattWellie
  1

• output_vcf

  #162 opened 3 years ago by Shreya-droid
  1

• Don't find the reference

  #161 opened 3 years ago by kangxiongbin
  1

• Failed to open or file not indexed:

  #158 opened 3 years ago by colinhercus
  0

• Ubuntu 20 compatible or Python 3 Version

  #155 opened 3 years ago by tahirasma
  1

• how can i get filtered position?

  #153 opened 3 years ago by ruizgo
  1

• python 2.x Sunset, potential 3.x port?

  #151 opened 3 years ago by OsborneACollin
  8

• --version option not working on pre.py and hap.py

  #156 opened 3 years ago by nvnieuwk
  0

• getting traceback while using '$python bin/hap.py'

  #149 opened 3 years ago by monika7697
  0

• Get something error in running the example.

  #148 opened 4 years ago by MartinChiaHsinLiu
  0

• Usage with different VCF callers

  #147 opened 4 years ago by stanleyrc
  1

• FP in phased variant overlapping non-phased variant

  #146 opened 4 years ago by arangrhie
  3

• Getting Error on Docker-compose

  #145 opened 4 years ago by puneetgaurrr
  0