biod/sambamba

Issues

• A Segmentation fault occurred in the sambamba markdup

  #520 opened 4 months ago by Xiangyue-Meng
  0

• sambamba markdup stuck in the finding positions of the duplicate reads in the file...

  #519 opened 6 months ago by xiechangxiao
  0

• sambamba (v. 0.8.0) sort: exit code 271

  #517 opened 7 months ago by jeffreycyyu
  0

• sambamba-markdup：(No space left on device)

  #509 opened a year ago by weirdo-onlooker
  1

• sambamba-sort: index [1] exceeds array of length 1

  #516 opened 8 months ago by ScienceAdvances
  0

• Sambamba slice - 94 Segmentation fault (core dumped)

  #515 opened a year ago by alexvasilikop
  2

• mpileup fail to execute bin/sh

  #514 opened a year ago by Axze-rgb
  0

• sambamba slice piped with sambamba view is having runtime problem when running in parallel

  #513 opened a year ago by yangyxt
  0

• problem of deduplication

  #512 opened a year ago by crazysummerW
  0

• Support removal of duplicates for paired-end reads

  #511 opened a year ago by rikrdo89
  0

• Difference of depth/mean coverage calculation among sambamba, bedtools, and mosdepth in high coverage panel data

  #510 opened a year ago by ipstone
  0

• sambamba 1.0.1 build failure

  #507 opened a year ago by chenrui333
  4

• conda sambamba 1.0 is running slower than conda sambamba 0.6

  #503 opened a year ago by ericpanyc
  1

• provide an example of pipping sambamba in documentation

  #504 opened a year ago by DrRLS
  1

• porting from old sambamba/BioD

  #502 opened a year ago by RichardCorbett
  1

• Sambamba subsample produces truncated BAMs

  #506 opened 2 years ago by Sven-Winter
  0

• Sambamba depth output repeats positions!

  #505 opened 2 years ago by Sven-Winter
  0

• sambamba-markdup: Unexpected '-' when converting from type string to type ulong

  #476 opened 4 years ago by ls233
  1

• sambamba-markdup: Range violation

  #501 opened 2 years ago by Cynthia1012
  2

• Minor subversion number missing in 1.0 release

  #500 opened 2 years ago by Stikus
  3

• Test suite error on Debian unstable

  #497 opened 2 years ago by tillea
  4

• Can you add sort by tag function?

  #499 opened 2 years ago by cherryamme
  1

• extends past source array of length 131072

  #498 opened 2 years ago by charliechen912ilovbash
  0

• sambamba -F "not duplicate" processed bam still have duplicated marked by sambamba markdup

  #477 opened 4 years ago by piyushjo15
  2

• sambamba depth region function add median value

  #494 opened 2 years ago by tamadezhenshiyuncai
  1

• sambamba depth region: Segmentation fault (core dumped)

  #492 opened 2 years ago by QichenFU
  0

• Feature request: Slice BAM file by query name

  #488 opened 3 years ago by yangyxt
  1

• Why does `sambamba sort` give me a different sort order across multiple runs (on the same BAM file)? Isn't `sort` by coordinates determinstic?

  #490 opened 2 years ago by etrh
  2

• depth region -L for multiple bam

  #491 opened 3 years ago by yuanjianwen-gif
  0

• Feature request: fixmate like samtools

  #489 opened 3 years ago by kaji331
  1

• can sambamba markdup give duprate concrete number?

  #487 opened 3 years ago by asmlgkj
  0

• sambamba --version's output doubled

  #486 opened 3 years ago by kim-fehl
  1

• `Samtools + libdeflate` out performs `sambamba` on a single thread

  #485 opened 3 years ago by mebbert
  3

• markdup - segmentation fault

  #483 opened 3 years ago by BioinfoRDX
  1

• Sambamba has remaining references to libbiod

  #484 opened 3 years ago by tillea
  9

• Cannot build 0.8.1 with Guix

  #482 opened 3 years ago by rekado
  7

• could not make sambamba-ldmd2-64

  #465 opened 3 years ago by An1e
  1

• do you support aggregation and dedup in one command?

  #481 opened 3 years ago by AlisaGU
  3

• sambamba markdup: Unable to write to stream

  #475 opened 3 years ago by sklages
  1

• MultiQC support for sambamba markdup

  #472 opened 4 years ago by gartician
  3

• sambamba markdup deadlock in Ubuntu 14.04

  #463 opened 4 years ago by dulunar
  3

• Compiling from source v.0.8.0 fails

  #473 opened 4 years ago by nadyawilliams
  2

• Inaccessible google groups support forum

  #474 opened 4 years ago by Poshi
  2

• sambamba merge using too much memory

  #470 opened 4 years ago by Poshi
  1

• downsampling by sambamba with seed

  #471 opened 4 years ago by dulunar
  1

• depth error

  #467 opened 4 years ago by Masaru-iehisa
  0

• additional header columns are removed

  #462 opened 4 years ago by tolot27
  1

• Is it necessary to sort bam files by read names before markdup?

  #466 opened 4 years ago by xiekunwhy
  0

• Sambamba should be able to convert SAM->BAM and sort at the same time like samtools

  #464 opened 4 years ago by moldach
  1

• markduplicate's result still differs from picard

  #461 opened 4 years ago by xiucz
  1