Issues

• Dockerfile: tzdata ask interactively ?

  adamewing/bamsurgeon#231 · Filter by author tetedange13 opened on Nov 17, 2025

• Single-end SV support beyond DEL/INS (follow-up to #210)

  adamewing/bamsurgeon#230 · Filter by author DayTimeMouse opened on Nov 15, 2025

• PROBLEM

  adamewing/bamsurgeon#229 · Filter by author phantom679 opened on Mar 17, 2025

• [E::bwa_idx_load_from_disk] fail to locate the index files

  adamewing/bamsurgeon#228 · Filter by author ATCG-ATCG opened on Sep 11, 2024
  1

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

  adamewing/bamsurgeon#225 · Filter by author TrangNg-Th opened on May 14, 2024

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

  adamewing/bamsurgeon#223 · Filter by author FelipeAze opened on Aug 7, 2023

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

  adamewing/bamsurgeon#217 · Filter by author ranjit58 opened on Jan 10, 2023
  8

• Samtools view issue

  adamewing/bamsurgeon#214 · Filter by author lukatop opened on Aug 25, 2022

• Add SV for Single end ONT reads

  adamewing/bamsurgeon#210 · Filter by author saranya-work opened on Aug 8, 2022
  3

• Publish docker image on Github Container Registry

  adamewing/bamsurgeon#209 · Filter by author holtgrewe opened on Jul 6, 2022
  2

• outbam

  adamewing/bamsurgeon#208 · Filter by author pengsl-lab opened on Jul 1, 2022
  7

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

  adamewing/bamsurgeon#207 · Filter by author oliverartz opened on Jun 20, 2022
  5

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

  adamewing/bamsurgeon#204 · Filter by author mkankain-hruh opened on May 20, 2022
  5

• Losing Haplotype information

  bug
  adamewing/bamsurgeon#195 · Filter by author FranziskaSundermann opened on Mar 21, 2022
  2

• no succesful mutations with addsv.py

  bug
  adamewing/bamsurgeon#191 · Filter by author Ashesltz opened on Dec 21, 2021

• All avgoutcoverage = 0

  bug
  adamewing/bamsurgeon#190 · Filter by author mrmilhaven opened on Dec 10, 2021
  4

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

  adamewing/bamsurgeon#186 · Filter by author gtollefson opened on Sep 1, 2021
  3

• Expansion repeats

  question
  adamewing/bamsurgeon#185 · Filter by author hadasApplied opened on Jul 17, 2021

• Less variant reads than expected with specified VAF

  adamewing/bamsurgeon#184 · Filter by author aldosr opened on Jul 13, 2021
  14

• DEL not considering VAF Input

  adamewing/bamsurgeon#183 · Filter by author jelisavetailic opened on Jul 8, 2021
  5

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

  adamewing/bamsurgeon#181 · Filter by author linkmonica opened on Jun 2, 2021
  2

• addsv Error missing bwatmp file

  adamewing/bamsurgeon#175 · Filter by author fre335 opened on Feb 9, 2021
  2

• Unsuccesful replacement of all reads

  adamewing/bamsurgeon#174 · Filter by author LauraVP1994 opened on Feb 8, 2021
  7

• ValueError: invalid coordinates: start > stop

  adamewing/bamsurgeon#173 · Filter by author pauline-ng opened on Feb 4, 2021
  1

• 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

  bug
  adamewing/bamsurgeon#169 · Filter by author andreiaamaral opened on Oct 20, 2020