Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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Make dockerfile build with htslib that was current at time of creation #118
Users need to clone or download repo archive so build is of known versions of code, not the master branch.