in read_utils.py::align_and_fix(), remove supplementary alignments before indel realignment #41
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…fore indel realignment in read_utils.py::align_and_fix(), remove supplementary alignments (i.e. chimeric reads) before indel realignment. Add an optional parameter, `--includeSupplementaryMappings` to perform indel realignment with supplementary mappings included.
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One question is whether the supplementary alignments are informative for real structural variation, and whether we may miss indels if we remove them. |
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I just noticed this! (oops) -- should we still merge this even though it seems we built in other workarounds? |
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in
read_utils.py::align_and_fix(), remove supplementary alignments (i.e. chimeric reads) before indel realignment. Add an optional parameter,--includeSupplementaryMappingsto perform indel realignment with supplementary mappings included.