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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Revert "Convert pindel to use the HTSlib API instead of the legacy sa… #13
Still some compilation issues - at the very least the INSTALL script does not work yet. Kai and I may be able to solve it, but I myself am back in only on Tuesday again. Temporary reverting this patch (which seems promising!) until either Kai can get a full fix with JMarshall's help or I can install the virtual box/linux and compile Pindel again so I can experiment with solutions myself.
Still some compilation issues - at the very least the INSTALL script does not work yet. Kai and I may be able to solve it, but I myself am back in only on Tuesday again. Temporary reverting this patch (which seems promising!) until either Kai can get a full fix with JMarshall's help or I can install the virtual box/linux and compile Pindel again so I can experiment with solutions myself.