adamewing/bamsurgeon

Issues

• Bamsurgeon addsnv.py takes 4 hours to add one SNP to a bam file of size 3.1MB ?

  #225 opened 2 months ago by TrangNg-Th
  0

• outbam

  #208 opened 2 years ago by pengsl-lab
  7

• Less variant reads than expected with specified VAF

  #184 opened 3 years ago by aldosr
  14

• "best contig too short to make mutation" / "No good alignment between mutated contig and original, aborting mutation!" Errors

  #223 opened a year ago by FelipeAze
  0

• [Enhancement] Specify vcf output path in addsv.py

  #218 opened a year ago by GuglielmoCerri
  0

• ValueError: quality and sequence mismatch: 98 != 97

  #204 opened 2 years ago by mkankain-hruh
  5

• Bamsurgeon goes silent (does not finish) on high coverage small panel bam file

  #217 opened a year ago by ranjit58
  8

• addindel.py error: Could not pile up over region - no successful mutations

  #186 opened 3 years ago by gtollefson
  3

• Samtools view issue

  #214 opened 2 years ago by lukatop
  0

• replace_reads.py only writing out one read of each pair for paired end.

  #212 opened 2 years ago by BrianOSullivanGit
  8

• Add SV for Single end ONT reads

  #210 opened 2 years ago by saranya-work
  3

• Release to pull in some new fixes

  #211 opened 2 years ago by apregier
  4

• AttributeError: 'array.array' object has no attribute 'tostring'

  #207 opened 2 years ago by oliverartz
  5

• Publish docker image on Github Container Registry

  #209 opened 2 years ago by holtgrewe
  0

• Dockerfile installation issue

  #205 opened 2 years ago by MaxSalm
  3

• no mate for...

  #157 opened 2 years ago by krishdb38
  2

• ValueError: invalid contig `22` addindel.py failed.

  #187 opened 2 years ago by shiying-sxu
  2

• Unexpected deletions around Inversion and Translocation

  #188 opened 2 years ago by mmiki21
  0

• trouble with a specific duplication

  #168 opened 2 years ago by RichardCorbett
  0

• sequence not present

  #177 opened 2 years ago by frankMusacchia
  2

• WARNING 2020-10-20 17:26:48,369 haplo_1_1167112_1167113 could not pileup for region: 1:1167103 WARNING 2020-10-20 17:27:46,108 1_1167103_1167198_None_None warning: no mate for hsa-mir-200b_MI0000342-s11000

  #169 opened 4 years ago by andreiaamaral
  0

• Installation problem

  #179 opened 2 years ago by joys8998
  2

• Expansion repeats

  #185 opened 3 years ago by hadasApplied
  0

• All avgoutcoverage = 0

  #190 opened 3 years ago by mrmilhaven
  4

• no succesful mutations with addsv.py

  #191 opened 3 years ago by Ashesltz
  0

• Losing Haplotype information

  #195 opened 2 years ago by FranziskaSundermann
  2

• Problem with postprocess.py changing read group IDs

  #156 opened 2 years ago by mairenileath
  2

• Learning

  #167 opened 2 years ago by prince-lab
  0

• Clarification on editing of MNVs

  #192 opened 2 years ago by ijhoskins
  2

• DEL not considering VAF Input

  #183 opened 3 years ago by jelisavetailic
  5

• Tumor - Matched normal

  #182 opened 3 years ago by jelisavetailic
  2

• Samtools error:[E::bam_hdr_write] Header too long for BAM format

  #181 opened 3 years ago by linkmonica
  2

• local variable 'tmpoutbamname' referenced before assignment

  #180 opened 3 years ago by YanaHrytsenko
  1

• Error running addsnv.py

  #178 opened 3 years ago by nuin
  0

• Unsuccesful replacement of all reads

  #174 opened 3 years ago by LauraVP1994
  7

• addsv Error missing bwatmp file

  #175 opened 3 years ago by fre335
  2

• addsnv: avgoutcover = 0 and no changes in output bam

  #176 opened 3 years ago by ruoyan-li
  4

• ValueError: invalid coordinates: start > stop

  #173 opened 3 years ago by pauline-ng
  1

• Reads for DEL not being excluded

  #171 opened 3 years ago by pauline-ng
  2

• addsv error: no successful mutations

  #172 opened 3 years ago by yifnzhao
  2

• Reducing bamsurgeon runtime.

  #170 opened 3 years ago by BrianOSullivanGit
  8

• sizes of successful CNVs - smaller than expected

  #166 opened 4 years ago by RichardCorbett
  5

• picard tools' FixMates returns error after spike-in and post-processing

  #162 opened 4 years ago by jmal0403
  2

• Dockerfile doesn't build

  #155 opened 4 years ago by cfriedline
  3

• Issues about the latest Dockerfile

  #165 opened 4 years ago by nikleotide
  0

• TCGA Mutation Calling Benchmark 4 Files

  #164 opened 4 years ago by popicka
  1

• no succesful mutations error

  #163 opened 4 years ago by kkamii
  0

• How is base quality for inserted bases determined?

  #161 opened 4 years ago by danrlu
  2

• pre-built container?

  #159 opened 4 years ago by RichardCorbett
  13

• Error in addsnv.py, "assert maxfrac is not None"

  #154 opened 4 years ago by fa8sanger
  3