I am using delly to call structural variants on a human WGS sample. I noticed that it finds certain variants that are essentially duplicates. For example:
chr4 177594033 DEL00005339 G <DEL> . PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chr4;END=177594095;PE=0;MAPQ=0;CT=3to5;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=5;SRQ=0.993243;CONSENSUS=GACAAAAACATATAAACAAATACAAATTATTATTATATGAAGGGTGAAAAATTATGTTCAGCTTTAATATTATGTGGCCTGAAACAAATTTGTATAAGTCATATGATCCGTTTTGTATATTCATTAAAATAGTCATAAAAATATAAAC;CE=1.75466 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/1:-51.3797,0,-42.791:10000:PASS:1115:1821:1820:1:0:0:23:27
chr4 177594033 DEL00005340 G <DEL> . PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chr4;END=177594095;PE=0;MAPQ=0;CT=3to5;CIPOS=-3,3;CIEND=-3,3;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=12;SRQ=0.994186;CONSENSUS=ATATAAACAAATACAAATTATTATTATATGAAGGGTGAAAAATTATGTTCAGCTTTAATATTATGTGGCCTGAAACAAATTTGTATAAGTCATATGATCCGTTTTGTATATTCATTAAAATAGTCATAAAAATATAAACAATGTAATAAGTATGTTTGAATAGTATTATGAT;CE=1.72637 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/1:-51.3797,0,-42.791:10000:PASS:1115:1821:1820:1:0:0:23:27
The two variants above have the same start position and the same end position (END=177594095). However, they differ in the SR, SRQ and CONSENSUS fields. These are defined in the VCF header as:
##INFO=<ID=SR,Number=1,Type=Integer,Description="Split-read support">
##INFO=<ID=SRQ,Number=1,Type=Float,Description="Split-read consensus alignment quality">
##INFO=<ID=CONSENSUS,Number=1,Type=String,Description="Split-read consensus sequence">
Of course, the consensus sequences are quite similar, but they aren't identical (I have simply added some spaces to the beginning of the 2nd sequence here to align them):
GACAAAAACATATAAACAAATACAAATTATTATTATATGAAGGGTGAAAAATTATGTTCAGCTTTAATATTATGTGGCCTGAAACAAATTTGTATAAGTCATATGATCCGTTTTGTATATTCATTAAAATAGTCATAAAAATATAAAC
ATATAAACAAATACAAATTATTATTATATGAAGGGTGAAAAATTATGTTCAGCTTTAATATTATGTGGCCTGAAACAAATTTGTATAAGTCATATGATCCGTTTTGTATATTCATTAAAATAGTCATAAAAATATAAACAATGTAATAAGTATGTTTGAATAGTATTATGAT
So what am I looking at here, exactly? If this is a deletion on chromosome 4 from position 177594033 to position 177594095, then how can the length of the consensus sequence be different? This is the "split read consensus", so presumably the sequence that appears to have been deleted based on how the reads covering that region are split. This means that these reads align to the genome with a gap and this gap indicates the deletion (image source):
Therefore, if the start and end position are the same, the consensus should also be identical. And, in any case, if the start and end positions are the same, then this should be the same structural variant, so why is it being reported twice? How can I interpret this result?
