genome/bam-readcount

Issues

• Inquiry on calculating avg_distance_to_effective_5p_end

  #111 opened 2 months ago by lykstudio
  1

• bam-readcount total count differs from igv total count

  #110 opened 2 months ago by aury98
  1

• result inconsistance

  #109 opened 3 months ago by sheenaseven
  0

• Bam-readcount running for an extremely long time

  #108 opened 3 months ago by lukaas33
  1

• [JOSS REVIEW] Minor edits to the github-based documentation

  #81 opened 3 years ago by friedue
  3

• NUL (\x00, ^@) and other control characters in output

  #107 opened 6 months ago by Kaddea
  4

• conda version different than github

  #106 opened a year ago by complexgenome
  1

• compilation failed

  #78 opened 3 years ago by lmanchon
  5

• Compilation Issue

  #102 opened 2 years ago by KevinYie
  3

• Questionably long runtime for RNA BAMs vs. DNA BAMs?

  #105 opened 2 years ago by seetarajpara
  0

• Interpretation of indels

  #104 opened 2 years ago by sakshamphul
  2

• Update bioconda deployment to Python3.7

  #59 opened 6 years ago by MatthewPorterGN
  2

• read depth incorrect

  #103 opened 2 years ago by bioscienceresearch
  2

• Reported depth not matching

  #101 opened 2 years ago by jcgrenier
  6

• Issue on installation

  #100 opened 3 years ago by idoit4fun
  0

• fatal error: compilation failed

  #99 opened 3 years ago by smoretti
  1

• Max depth 8000

  #69 opened 3 years ago by LauraVP1994
  1

• Make Error for boost on MacOS

  #77 opened 3 years ago by chintan-vora-tfs
  4

• Run without errors but failed to produce the site list

  #64 opened 5 years ago by drtamermansour
  8

• Identify reads aligned to mutant and wild type sequences

  #98 opened 3 years ago by rpauly
  1

• `bam-readcount` build from release source code zip/tarball does not have a version number

  #96 opened 3 years ago by apldx
  0

• how to get the site list for indels?

  #92 opened 3 years ago by breezetown
  3

• [JOSS REVIEW] Any functionality documentation?

  #84 opened 3 years ago by bebatut
  2

• [JOSS REVIEW] Missing the community contribution guidelines

  #83 opened 3 years ago by bebatut
  2

• [JOSS REVIEW] Example usage

  #80 opened 3 years ago by friedue
  6

• [JOSS REVIEW] minor edits to the manuscript

  #82 opened 3 years ago by friedue
  3

• how to get a region file

  #90 opened 3 years ago by stroke1989
  3

• Support for BAM CSI index

  #89 opened 3 years ago by f-huber
  1

• Error when path_to_bam have bam in middle

  #88 opened 3 years ago by sssimonyang
  0

• [JOSS REVIEW] docker documentation

  #79 opened 3 years ago by friedue
  3

• Inconsistent output

  #87 opened 3 years ago by mnshgl0110
  2

• WARNING

  #86 opened 3 years ago by stroke1989
  3

• Reason for low coverage output for deepseq data

  #85 opened 3 years ago by YashaNazirB
  5

• Compilation fails because of missing -fPIC

  #75 opened 3 years ago by SethosII
  2

• Update included samtools and boost

  #65 opened 5 years ago by serge2016
  3

• Only counting multiple aligned reads for one chromosome with "-l *.bed" and "-q 0" parameters

  #72 opened 4 years ago by Adglink
  5

• fpfilter.pl - failed to get readcounts for variant allele

  #71 opened 4 years ago by Souzavgp
  0

• Fail to open BAM file –q

  #70 opened 4 years ago by Souzavgp
  3

• Getting the read names/ IDs?

  #68 opened 4 years ago
  4

• Distance to both 5' and 3' ends

  #67 opened 5 years ago by matnguyen
  0

• Is there a recommended citation for this tool?

  #66 opened 5 years ago by whtns
  1

• missing avg_distance_to_effective_3p_end

  #63 opened 6 years ago by stemangiola
  0

• Feature request: Request for unmapped region option

  #62 opened 6 years ago by ankit4035
  2

• a question of how to use bam-readcount on insertions?

  #57 opened 6 years ago by rayliu0115
  1

• fail to load bam index

  #61 opened 6 years ago by mcfog1
  0

• make test fails RunBamReadcount (python vs python2)

  #60 opened 6 years ago by darked89
  0

• print-individual-mapq not working

  #58 opened 6 years ago by fkokocinski
  2

• [bam_plp_destroy] memory leak: 1. Continue anyway.

  #56 opened 6 years ago by jflucier
  1

• Inconsistent output when run with or without bed file for regions

  #55 opened 7 years ago by juliandangelo
  0

• Deletion counts behaviour

  #54 opened 7 years ago by iranmdl
  3