Closed mwalker174 closed 4 months ago
Addresses a known bug in CollectSVEvidence when encountering an alignment consisting of a single insertion, i.e. a 151I cigar. This causes the CollectSVEvidence GATK tool to throw an error:
CollectSVEvidence
a 151I
java.lang.IllegalArgumentException: Invalid interval. Contig:chr2 start:644282 end:644281
A workaround is to enable GATK's NonZeroReferenceLengthAlignmentReadFilter.
NonZeroReferenceLengthAlignmentReadFilter
Tested on 5 samples from the 1KGP reference panel and confirmed bit-wise parity on all (decompressed) outputs.
Addresses a known bug in
CollectSVEvidencewhen encountering an alignment consisting of a single insertion, i.e.a 151Icigar. This causes theCollectSVEvidenceGATK tool to throw an error:A workaround is to enable GATK's
NonZeroReferenceLengthAlignmentReadFilter.Tested on 5 samples from the 1KGP reference panel and confirmed bit-wise parity on all (decompressed) outputs.