Issues

• Abra2 collapses genomic duplication in assembly, leading to false realignments

  mozack/abra2#66 · Filter by author fbattke opened on Jun 18, 2025

• Realignment Error example for small duplication

  mozack/abra2#65 · Filter by author camillebenoist opened on Mar 17, 2025

• Possible issues for large genome (No index is available for this BAM file. and exceeding integer length in GTF file)

  mozack/abra2#64 · Filter by author JuiTse opened on Jan 17, 2025

• abra2 error java.lang.NumberFormatException

  mozack/abra2#63 · Filter by author C-YONG opened on Dec 4, 2024

• Window size vs targets - using targets only?

  mozack/abra2#62 · Filter by author ranasats opened on Nov 20, 2024
  3

• Abra2-processed bams are incompatible with Strelka2

  mozack/abra2#61 · Filter by author lculibrk opened on Apr 10, 2024

• Specific case that ABRA2 is not realigning correctly

  mozack/abra2#60 · Filter by author parsaeskandar opened on Feb 12, 2024

• IndelRealigner-parameters vs Abra2-parameters

  mozack/abra2#59 · Filter by author Manuel-DominguezCBG opened on Nov 9, 2023
  1

• How to shorten run time

  mozack/abra2#58 · Filter by author jingjing578 opened on Oct 13, 2023
  4

• build fails on linux

  mozack/abra2#57 · Filter by author yangxingyu588 opened on Sep 9, 2023

• Unknown format conversion exception

  mozack/abra2#56 · Filter by author abhiku0007 opened on Aug 26, 2023
  1

• Fusions

  mozack/abra2#55 · Filter by author gitMakeCoffee opened on Mar 24, 2023

• Abra2 creating large (around 100bp) deletions to alignment

  mozack/abra2#54 · Filter by author rchapman2000 opened on Mar 6, 2023
  2

• java.lang.OutOfMemoryError: Java heap space

  mozack/abra2#52 · Filter by author AdilyAid opened on Sep 11, 2022
  1

• Abra and log4j

  mozack/abra2#51 · Filter by author colindaven opened on Dec 14, 2021

• Score threshold and content of the printed INFO

  mozack/abra2#49 · Filter by author camillebenoist opened on Nov 12, 2021

• java.lang.IllegalArgumentException: Invalid reference index -1

  mozack/abra2#48 · Filter by author ThanosPAS opened on Oct 14, 2021
  1

• v2.24 gives "Error loading: libAbra.so", older versions do not

  mozack/abra2#46 · Filter by author chrisamiller opened on Sep 15, 2021
  7

• max_paths_from_root

  mozack/abra2#45 · Filter by author warthmann opened on Aug 23, 2021
  3

• Num reads to scan for read length/insert length/mapq

  mozack/abra2#44 · Filter by author danoreper opened on Jun 7, 2021

• Bed file format

  mozack/abra2#43 · Filter by author V-Catherine opened on Jun 18, 2020
  1

• feature request: stdin functionality

  mozack/abra2#42 · Filter by author eboyden opened on Feb 29, 2020

• Realigned output bam TLEN field plus/minus sign when FLAG == 147

  mozack/abra2#40 · Filter by author Julie-Zhongyun-Huang opened on Jan 16, 2020
  2

• Compilation on Mac

  mozack/abra2#38 · Filter by author edgardomortiz opened on Aug 15, 2019
  1

• compilation terminated during make

  mozack/abra2#37 · Filter by author zhoutengsheng opened on Jul 21, 2019
  3