Illumina/GTCtoVCF

Issues

• Empty ALT genotypes?

  #81 opened 6 months ago by rajwanir
  1

• Tool assumptions and behaviour

  #80 opened 7 months ago by rajwanir
  6

• Any workaround for missing RefStrand and SourceSeq column in the manifest?

  #78 opened 7 months ago by rajwanir
  7

• SB calculation

  #77 opened a year ago by marissa97
  1

• Any experience about GQ settings

  #76 opened a year ago by AliceCheng7
  1

• ERROR - Reference is missing entry for chromosome 3

  #72 opened 3 years ago by HoneeeyBee
  2

• About ImportError: No module named vcf.parser

  #32 opened 6 years ago by JeonHyungJin
  5

• Python3 support

  #71 opened 3 years ago by Stikus
  1

• Python3 Question

  #65 opened 4 years ago by tbrunetti
  3

• VCF REF column outputting in bytes instead of string

  #69 opened 3 years ago by rarsenal
  3

• GQ score clarification

  #68 opened 4 years ago by Derrup
  3

• Bus error when converting GTC to VCF

  #67 opened 4 years ago by khzhu
  7

• Please create setup.py

  #17 opened 6 years ago by dbrami
  2

• Limitations of --output-vcf-path and --log-file

  #15 opened 6 years ago by freeseek
  4

• GTC converter - WARNING - Reference is missing entry for chromosomes

  #38 opened 6 years ago by cbiOPela
  8

• Illumina Generated Manifest has no RefStrand column

  #49 opened 5 years ago by tbrunetti
  5

• Reference not detected if lowercase characters

  #64 opened 4 years ago
  4

• Precision difference when updating numpy versions

  #42 opened 5 years ago by jjzieve
  0

• Replace ID in output VCF with `--id` option

  #50 opened 5 years ago by stephenturner
  0

• Unclear Error message

  #59 opened 5 years ago by brianyiktaktsui
  1

• SourceSeq validation failures should be skipped instead of erroring out

  #66 opened 4 years ago by jjzieve
  0

• Next release

  #60 opened 5 years ago by varuna-sd
  2

• download_reference script has broken links

  #62 opened 5 years ago by jjzieve
  2

• GQ type is "String" instead of "Float"

  #51 opened 5 years ago by kmhernan
  1

• download_reference.sh is outdated

  #54 opened 5 years ago by moranr7
  3

• Unable to run download_reference.sh on Mac

  #55 opened 5 years ago by biying-orig3n
  3

• GTC parser error : All GT values in converted vcf are './.'

  #48 opened 5 years ago by gezthxbio
  4

• Merging B allele frequency and log R ratio for multiple BPMRecords

  #19 opened 5 years ago by brianhill11
  12

• BAF and LRR

  #14 opened 5 years ago by freeseek
  3

• Indel haploid calls printed as diploid

  #21 opened 5 years ago by brianhill11
  2

• scripts/download_reference.sh fails when missing `realpath`

  #35 opened 6 years ago by GvandeSteeg
  0

• .vcf format for BaseSpace Variant Interpreter?

  #37 opened 6 years ago by cbiOPela
  0

• 3 things: iteritems() vs items(); rect to polar; sorting errors

  #26 opened 6 years ago by dmcgoldrick
  6

• Contig header and Chrom record order do not match reference order

  #28 opened 6 years ago by brmyers
  1

• Discrepancies with the VCF Specification

  #27 opened 6 years ago by brmyers
  3

• vcf.parser error

  #25 opened 6 years ago by biopelayo
  1

• error in mainifest

  #23 opened 6 years ago by dora201888
  1

• Unable to convert some variants

  #18 opened 6 years ago by ns3116
  1

• logs usage of BPM file when CSV is invoked

  #16 opened 6 years ago by dbrami
  2

• using conda, can't get it to work because of some python bug

  #13 opened 7 years ago by martiliasf
  5

• call rate filtering

  #12 opened 7 years ago by stephenturner
  2

• Script reports that reference has missing chromosome 6

  #8 opened 7 years ago by YourLogoHere
  4

• Error using manifest in CSV format

  #6 opened 7 years ago by smparsons96
  2

• better documentation on `--unsquash-duplicates`

  #4 opened 7 years ago by stephenturner
  6

• reduce manifest to extract subset?

  #1 opened 7 years ago by stephenturner
  8

• Reference allele is not queried for locus

  #2 opened 7 years ago by stephenturner
  1