biobambam: tools for read pair collation based algorithms on BAM files

@inproceedings{Tischler2013biobambamTF,
  title={biobambam: tools for read pair collation based algorithms on BAM files},
  author={German Tischler and Steven Leonard},
  booktitle={Source Code for Biology and Medicine},
  year={2013}
}
Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped data and the reference or of variants within the mapped data. In this order paired reads are usually separated in the file, which complicates some other applications like duplicate marking or conversion to the FastQ format which require to access the full… CONTINUE READING
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