hall-lab/svtools

Issues

• vcftobedpe does not give strandedness for MANTA Outputs

  #330 opened 7 months ago by think-o
  1

• Svtools classify BNDing most of the DELs

  #298 opened 5 years ago by brittanyhowell
  1

• GT:CN ./.:309.986

  #332 opened 5 months ago by pingxinxing
  0

• [E::vcf_parse_format] Incorrect number of FORMAT fields at chrxxxx

  #331 opened 7 months ago by pingxinxing
  0

• svtools copynumber:Can't find directory 'bin_1000'.

  #329 opened 7 months ago by pingxinxing
  0

• svtools lsort KeyError: 'CIPOS'

  #328 opened 9 months ago by hcsun1
  0

• Assistance Needed with svtools lsort - No Output Generated

  #327 opened a year ago by karen916
  0

• svtools vcfpaste error

  #310 opened 4 years ago by KrithikaSubramanian
  2

• Installation error with Pip because some packages rely on Python3

  #300 opened 5 years ago by shangshanzhizhe
  2

• svtools afreq KeyError: 'SQ' in

  #326 opened 2 years ago by shameem356
  0

• ValueError: max() arg is an empty sequence

  #325 opened 2 years ago by Hubuyan
  0

• lsort Index error

  #316 opened 3 years ago by stubbsrl
  3

• bedpetovcf does not work with vcftobedpe output as input

  #324 opened 3 years ago by anoronh4
  1

• svtools copynumber error *** Break *** segmentation violation

  #323 opened 3 years ago by cusanchang
  0

• Not able to convert vcf to bedpe (Manta output)

  #322 opened 3 years ago by Giuseppe1995
  0

• MEI annotations and list index out of range while classifying deletions

  #320 opened 3 years ago by jasonbhn
  0

• possible bug in TRA conversion

  #318 opened 3 years ago by anoronh4
  0

• Are lmerge same as l_merge.py scripts included in LUMPY?

  #317 opened 3 years ago by sulinq
  0

• merge error

  #299 opened 5 years ago by lee039
  2

• lmerge divide zero error

  #315 opened 3 years ago by genostack
  2

• Installation still fails due to conflicting pandas version

  #314 opened 3 years ago by Carina201000
  0

• what is the difference between lmerge sum and prod algorithm ?

  #313 opened 3 years ago by genostack
  0

• Installation fails due to conflicting pandas version

  #302 opened 5 years ago by NeolithEra
  6

• pip install fails

  #312 opened 3 years ago by anoronh4
  2

• No module named 'l_bp'

  #309 opened 4 years ago by Avramis
  1

• build high confidence call set for training

  #285 opened 5 years ago by edg1983
  0

• vcftobedpe complains about no END field in LUMPY BNDs.

  #307 opened 4 years ago by jasonbhn
  1

• Python 3.6

  #308 opened 4 years ago by mike-molnar
  0

• Genotyping skips insertions (INS)

  #306 opened 4 years ago by hellebaa
  0

• Does svtools support to mapping BEDPE to human genes?

  #305 opened 4 years ago by Shicheng-Guo
  0

• Syntax error msg

  #304 opened 4 years ago by nitha26
  0

• I tried run smoove but encountered the error below with the exit status: 83

  #303 opened 4 years ago by MaoSihong
  0

• vcftobedpe's output has one-based START coordinates instead of one-based

  #301 opened 5 years ago by ManavalanG
  1

• Not clear with the command to run svtools

  #276 opened 5 years ago by amrita1983
  2

• Running SV-tools across combined VCFs with multiple SV call types

  #291 opened 5 years ago by oalavijeh
  1

• svtools lsort

  #297 opened 5 years ago by marquispa
  2

• bedpetovcf crashes

  #296 opened 5 years ago by johnemajor
  1

• Svtools copynumber error

  #287 opened 5 years ago by deepalivasoya
  1

• prune's RETAINED criteria

  #295 opened 5 years ago by pmonnahan
  0

• Svtools classify raising ValueError exception

  #294 opened 5 years ago by yachenhu
  0

• Svtyper, svtyper-sso and svtools genetype output discrepant genotypes

  #293 opened 5 years ago by yachenhu
  0

• Clarification on classifier use and output

  #288 opened 5 years ago by edg1983
  0

• lsort sorting?

  #284 opened 5 years ago by jjfarrell
  2

• vcftobedpe fails for certain MANTA calls

  #281 opened 6 years ago by axelgschwind
  0

• Genotypes all converted to ./.

  #277 opened 6 years ago by gwct
  3

• Difference between lmerge and prune?

  #280 opened 6 years ago by gwct
  2

• Breakpoint positions in BEDPE file converted from lumpy vcf output are not 0-based

  #275 opened 6 years ago by SilenWang
  2

• how to run svtools

  #279 opened 6 years ago by Jordi-V
  0

• lsort doest not merge multisamples run by lumpy

  #274 opened 6 years ago by Jordi-V
  3

• IndexError: list index out of range svtools copynumber

  #273 opened 6 years ago by arumds
  0