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Description
Dears,
I've been using the smoove software for structural variant detection recently, and I have some questions regarding the BND-type results, for example:
chr1 89121966 5132_1 N [chr21:45417197[N 158.48 . SVTYPE=BND;STRANDS=--:18;CIPOS=-5,3;CIEND=-5,3;CIPOS95=0,0;CIEND95=0,0;MATEID=5132_2;EVENT=5132;SU=18;PE=11;SR=7;PRPOS=8.67888e-15,5.63759e-12,3.65994e-09,2.37502e-06,0.00154108,0.998107,0.0003497,1.22516e-07,4.28944e-11;PREND=8.299e-15,5.43655e-12,3.56137e-09,2.33218e-06,0.00152636,0.997584,0.000886034,7.86724e-07,6.98693e-10;AC=1;AN=2 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:158:158.48:-25,-9,-50:80:65:14:64:13:35:3:0:29:10:0.17
chr21 45417197 5132_2 N [chr1:89121966[N 158.48 . SVTYPE=BND;STRANDS=--:18;CIPOS=-5,3;CIEND=-5,3;CIPOS95=0,0;CIEND95=0,0;MATEID=5132_1;EVENT=5132;SECONDARY;SU=18;PE=11;SR=7;PRPOS=8.299e-15,5.43655e-12,3.56137e-09,2.33218e-06,0.00152636,0.997584,0.000886034,7.86724e-07,6.98693e-10;PREND=8.67888e-15,5.63759e-12,3.65994e-09,2.37502e-06,0.00154108,0.998107,0.0003497,1.22516e-07,4.28944e-11;AC=1;AN=2 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB0/1:158:158.48:-25,-9,-50:80:65:14:64:13:35:3:0:29:10:0.17
Based on the results above, we know it is a translocation event involving DNA segments. According to the specifications in the VCFv4.3.pdf document, we also know that one of the fragments is joined in reverse-complement orientation to the other segment. Given this, could this event represent both a translocation and an inversion?