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Illumina / manta

Structural variant and indel caller for mapped sequencing data
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Crash on complex indels at read end #169

Closed mozack closed 5 years ago

mozack commented 5 years ago

Hi,

Manta appears to exit when a read partially overlaps a complex indel.

i.e. A read with a cigar similar to the following: 92M6D8I

These reads are valid, conform to the SAM spec and can represent real variation.

Please see a snippet from the log file below.

Thanks!

[2019-01-29T16:40:55.043925Z] [hm1-pvt.bioinf.unc.edu] [37268_1] [WorkflowRunner] [ERROR] [2019-01-29T16:40:24.038018Z] [hm1-pvt.bioinf.unc.edu] [37268_1] [makeLocusGraph_chromId_006_chr7_0006] ERROR: Exception caught while processing single read record: [2019-01-29T16:40:55.043925Z] [hm1-pvt.bioinf.unc.edu] [37268_1] [WorkflowRunner] [ERROR] [2019-01-29T16:40:24.039144Z] [hm1-pvt.bioinf.unc.edu] [37268_1] [makeLocusGraph_chromId_006_chr7_0006] HWI-D00119:50:H7AP8ADXX:1:2214:4623:36632/2 tid:pos:strand 6:76259991:+ cigar: 92M6D8I templSize: 285 mate_tid:pos:strand 6:76260175:- [2019-01-29T16:40:55.043925Z] [hm1-pvt.bioinf.unc.edu] [37268_1] [WorkflowRunner] [ERROR] [2019-01-29T16:40:24.139682Z] [hm1-pvt.bioinf.unc.edu] [37268_1] [makeLocusGraph_chromId_006_chr7_0006] FATAL_ERROR: 2019-Jan-29 11:40:24 /builder/src/c++/lib/manta/SVLocusScanner.cpp(454): Throw in function void getSVCandidatesFromReadIndels(const ReadScannerOptions&, const ReadScannerDerivOptions&, const SimpleAlignment&, const bam_header_info&, SourceOfSVEvidenceInDNAFragment::index_t, std::vector&) [2019-01-29T16:40:55.043925Z] [hm1-pvt.bioinf.unc.edu] [37268_1] [WorkflowRunner] [ERROR] [2019-01-29T16:40:24.142326Z] [hm1-pvt.bioinf.unc.edu] [37268_1] [makeLocusGraph_chromId_006_chr7_0006] Dynamic exception type: boost::exception_detail::clone_impl [2019-01-29T16:40:55.043925Z] [hm1-pvt.bioinf.unc.edu] [37268_1] [WorkflowRunner] [ERROR] [2019-01-29T16:40:24.143274Z] [hm1-pvt.bioinf.unc.edu] [37268_1] [makeLocusGraph_chromId_006_chr7_0006] std::exception::what: Can't process unexpected alignment pattern: alignment: 6:76259991+ 92M6D8I

ctsa commented 5 years ago

Thanks for the report, unfortunately we haven't seen this pattern from any of the standard mappers we support, so I don't think this would be addressed anytime soon. If a patch is submitted which implements a simple workaround like converting these segments to soft-clip we might be able to incorporate it.