Insertions with Incomplete Insert Sequence Assembly

Large insertions are reported in some cases even when the insert sequence cannot be fully assembled. In this case, the SV Caller reports the insertion using the <INS> symbolic allele and includes the special INFO fields LEFT_SVINSSEQ and RIGHT_SVINSSEQ to describe the assembled left and right ends of the insert sequence. The following is an example of such a record from the joint diploid analysis of NA12878, NA12891 and NA12892 mapped to hg19:

chr1 11830208 MantaINS:1577:0:0:0:3:0 T <INS> 999 PASS END=11830208;SVTYPE=INS;CIPOS=0,12;CIEND=0,12;HOMLEN=12;HOMSEQ=TAAATTTTTCTT;LEFT_SVINSSEQ=TAAATTTTTCTTTTTTCTTTTTTTTTTAAATTTATTTTTTTATTGATAATTCTTGGGTGTTTCTCACAGAGGGGGATTTGGCAGGGTCACGGGACAACAGTGGAGGGAAGGTCAGCAGACAAACAAGTGAACAAAGGTCTCTGGTTTTCCCAGGCAGAGGACCCTGCGGCCTTCCGCAGTGTTCGTGTCCCTGATTACCTGAGATTAGGGATTTGTGATGACTCCCAACGAGCATGCTGCCTTCAAGCATCTGTTCAACAAAGCACATCTTGCACTGCCCTTAATTCATTTAACCCCGAGTGGACACAGCACATGTTTCAAAGAG;RIGHT_SVINSSEQ=GGGGCAGAGGCGCTCCCCACATCTCAGATGATGGGCGGCCAGGCAGAGACGCTCCTCACTTCCTAGATGTGATGGCGGCTGGGAAGAGGCGCTCCTCACTTCCTAGATGGGACGGCGGCCGGGCGGAGACGCTCCTCACTTTCCAGACTGGGCAGCCAGGCAGAGGGGCTCCTCACATCCCAGACGATGGGCGGCCAGGCAGAGACACTCCCCACTTCCCAGACGGGGTGGCGGCCGGGCAGAGGCTGCAATCTCGGCACTTTGGGAGGCCAAGGCAGGCGGCTGCTCCTTGCCCTCGGGCCCCGCGGGGCCCGTCCGCTCCTCCAGCCGCTGCCTCC GT:FT:GQ:PL:PR:SR 0/1:PASS:999:999,0,999:22,24:22,32 0/1:PASS:999:999,0,999:18,25:24,20 0/0:PASS:230:0,180,999:39,0:34,0