sanger-pathogens/snp-sites

Issues

• why snp-sites generated variations numbers different snippy mapping results

  #113 opened 3 months ago by Zjianglin
  0

• Warning: No SNPs were detected so there is nothing to output

  #112 opened a year ago by sreerampeela
  1

• error: alignment contains sequences of unequal length

  #101 opened 4 years ago by rderelle
  8

• 32 bit signed integer error

  #95 opened 4 years ago by ethering
  1

• segmentation fault

  #110 opened a year ago by BettyAC
  2

• What does *STAR* in ALT stand for

  #105 opened 3 years ago by jielab
  3

• Build is failing on Mac OS

  #45 opened 9 years ago by bouzidnm
  3

• How to know the interested SNP position in genome?

  #111 opened a year ago by snackens
  0

• How to specify the reference sequence

  #109 opened 2 years ago by ACColin
  0

• snp-sites do not see do deletion events

  #94 opened 4 years ago by bioinfornatics
  1

• Keeping indels, projecting reference coordinates?

  #66 opened 7 years ago by LovellHAGSC
  1

• ./configure: line 3036: syntax error near unexpected token `CHECK,check' ./configure: line 3036: `PKG_CHECK_MODULES(CHECK,check >= 0.8.2,have_check="yes",'

  #108 opened 2 years ago by nick-pestell
  0

• Possibility to specify known reference

  #90 opened 4 years ago by jcgrenier
  2

• Recommendation for multiple genome alignment

  #106 opened 3 years ago by snayfach
  1

• How to understand `monomorphic sites`?

  #107 opened 3 years ago by xuechunxu
  1

• snp-sites for all ~2 million SARS-COV-2 genomes in GISAID

  #104 opened 3 years ago by jielab
  1

• Warning: No SNPs were detected so there is nothing to output

  #96 opened 4 years ago by pgcudahy
  1

• functionality of -b option alone?

  #82 opened 5 years ago by eam12
  1

• Output invariant sites and nucleotide frequencies

  #62 opened 7 years ago by EpiDemos82
  5

• Improvement: let user specify pure and ambiguous bases

  #103 opened 3 years ago by arturotorreso
  0

• snp-sites docker install issue

  #102 opened 3 years ago by AgatheJouet
  0

• Missing data in vcf output format

  #64 opened 7 years ago by MafaldaSFerreira
  2

• Is there a way to extract SNP mutations form the VCF file ?

  #99 opened 4 years ago by ASQWZXED
  0

• How to manage heterozygosity in SNP conversion?

  #98 opened 4 years ago by Pryfed
  0

• snp-sites -c doesn't produce recognisable alignment for IQtree

  #97 opened 4 years ago by martinastoycheva
  1

• specify order of output of -C option in help message

  #88 opened 5 years ago by amilesj
  2

• snps-sites tool help

  #93 opened 4 years ago by cmaquez
  0

• how to visualize VCF file in artemis?

  #91 opened 4 years ago by tushar-ahmed
  0

• Info in VCF output format

  #68 opened 6 years ago by ricardoruiz2897
  1

• apt-get installation of snp-sites

  #89 opened 4 years ago by nbawe
  1

• line 3030: syntax error near unexpected token `CHECK,check' on REHL 7.5

  #81 opened 5 years ago by Aworwui
  1

• Segmentation error

  #78 opened 5 years ago by besnarda
  1

• Error with Mauve alignment input

  #77 opened 5 years ago by jglenn72
  1

• Is the reference genome used when using the snp-sites software?

  #79 opened 5 years ago by youlijun
  1

• Is there a sequence length limit? "Warning: No SNPs were detected so there is nothing to output."

  #80 opened 5 years ago by FatihSarigol
  1

• Problem with installation via Bioconda

  #83 opened 5 years ago by Martinique-F
  2

• Pipe into snp-sites

  #76 opened 6 years ago by ssjunnebo
  0

• SegFault for unknown reason

  #72 opened 6 years ago by flashton2003
  1

• Recommended workflow?

  #71 opened 6 years ago by stevendavis
  0

• No ./configure in release tarball despite docs

  #69 opened 6 years ago by tseemann
  0

• Docker file typo

  #60 opened 7 years ago by tseemann
  1

• Print to screen

  #63 opened 7 years ago by robynslee
  2

• Gaps not reported in output?

  #61 opened 7 years ago by mgalardini
  2

• Segmentation fault with larger sequences (on Desktop and HPC)

  #57 opened 7 years ago by CMWbio
  3

• segmentation fault with `-b` option

  #58 opened 7 years ago by kwongj
  4

• brew recipe needs to be updated to the latest release.

  #55 opened 8 years ago by andersgs
  2

• Linuxbrew installation issue (links issue)

  #54 opened 8 years ago by rbutleriii
  1

• segmentation fault in one fasta but not on the other

  #53 opened 8 years ago by hongsamL
  5

• Didn't mean to open this

  #52 opened 8 years ago by tseemann
  1

• Failing tests on various platforms

  #51 opened 8 years ago by satta
  3