I came across the following error when running manta
"
GenerateSVCandidates: /builder/src/c++/lib/applications/GenerateSVCandidates/SVCandidateAssemblyRefiner.cpp:342: void addCigarToSpanningAlignment(SVCandidate&): Assertion `insertSize || deleteSize' failed.
"
I checked the file failed (candidateSV.*.vcf) and found the following lines at the end.
chr12 52870970 MantaDEL:69068:0:0:0:0:0 ATGTGTGTG A . . END=52870978;SVTYPE=DEL;SVLEN=-8;CIGAR=1M8D;CIPOS=0,23;HOMLEN=23;HOMSEQ=TGTGTGTGTGTGTGTGTGTGTGT;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0
chr12 52870970 MantaDEL:69069:0:0:0:0:0 ATGTGTGTG A . . END=52870978;SVTYPE=DEL;SVLEN=-8;CIGAR=1M8D
It seems that there is something wrong when parsing the DEL at the end.
I used the default parameters.
Shall I tune some parameters to make the run succeed?
Thanks.
Hi,
I came across the following error when running manta " GenerateSVCandidates: /builder/src/c++/lib/applications/GenerateSVCandidates/SVCandidateAssemblyRefiner.cpp:342: void addCigarToSpanningAlignment(SVCandidate&): Assertion `insertSize || deleteSize' failed. "
I checked the file failed (candidateSV.*.vcf) and found the following lines at the end. chr12 52870970 MantaDEL:69068:0:0:0:0:0 ATGTGTGTG A . . END=52870978;SVTYPE=DEL;SVLEN=-8;CIGAR=1M8D;CIPOS=0,23;HOMLEN=23;HOMSEQ=TGTGTGTGTGTGTGTGTGTGTGT;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0 chr12 52870970 MantaDEL:69069:0:0:0:0:0 ATGTGTGTG A . . END=52870978;SVTYPE=DEL;SVLEN=-8;CIGAR=1M8D
It seems that there is something wrong when parsing the DEL at the end. I used the default parameters. Shall I tune some parameters to make the run succeed? Thanks.