title: BamHash: a checksum program for verifying the integrity of sequence data.
abstract: CONCLUSIONS
  Large resequencing projects require a significant amount of storage for raw sequences, as well as alignment files. Because the raw sequences are redundant once the alignment has been generated, it is possible to keep only the alignment files. We present BamHash, a checksum based method to ensure that the read pairs in FASTQ files match exactly the read pairs stored in BAM files, regardless of the ordering of reads. BamHash can be used to verify the integrity of the files stored and discover any discrepancies. Thus, BamHash can be used to determine if it is safe to delete the FASTQ files storing raw sequencing read after alignment, without the loss of data.
  
  
  METHODS
  The software is implemented in C++, GPL licensed and available at https://github.com/DecodeGenetics/BamHash
  
  
  BACKGROUND
  pmelsted@hi.is.
authors.affiliation: deCODE Genetics/Amgen, Reykjavík, Iceland and.
authors.forename: Arna
authors.initials: A
authors.lastname: Óskarsdóttir
authors.affiliation: deCODE Genetics/Amgen, Reykjavík, Iceland and.
authors.forename: Gísli
authors.initials: G
authors.lastname: Másson
authors.affiliation: deCODE Genetics/Amgen, Reykjavík, Iceland and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavík, Iceland.
authors.forename: Páll
authors.initials: P
authors.lastname: Melsted
mesh_terms: D006801:Humans; D015203:Reproducibility of Results; D017421:Sequence Analysis; D012984:Software; D013223:Statistics as Topic