Can HyDe be used to analyze datasets containing structural variants (SVs) and insertions/deletions (InDels)?

[qy152]

Hi, can HyDe be used to analyze datasets containing structural variants (SVs) and insertions/deletions (InDels)?sv format is:
Chr01 553780 MantaDEL:55:0:0:0:0:0 GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA G 1020 PASS . GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO 0/
0:001:65:138,0:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 0/0:001:65:41,0:+-:1020:DEL:MantaDEL
_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 0/0:001:65:52,0:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTG
GGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 0/0:001:65:115,0:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATA
CTTGCTATAAACA:G:Chr01_553780-Chr01_553845 0/0:001:65:155,0:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01
553845 0/0:001:65:149,0:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 0/0:001:65:206,0:+-:
1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 0/0:001:65:117,0:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGG
TGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 0/0:001:65:198,0:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGT
GAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 0/0:001:65:111,0:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Ch
r01_553780-Chr01_553845 0/0:001:65:92,0:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 0/0:
001:65:95,0:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 0/0:001:65:116,0:+-:1020:DEL:MantaDEL
55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 0/0:001:65:90,0:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGG
TTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 0/0:001:65:83,0:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTT
GCTATAAACA:G:Chr01_553780-Chr01_553845 0/0:001:65:105,0:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_5
53845 0/0:001:65:93,0:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 0/0:001:65:195,0:+-:10
20:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 0/0:001:65:48,0:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGC
CACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 1/1:001:65:0,19:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAA
GGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 1/1:001:65:0,21:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01
553780-Chr01_553845 1/1:001:65:0,34:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 1/1:00
1:65:0,48:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 1/1:001:65:0,17:+-:1020:DEL:MantaDEL_55
0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 1/1:001:65:0,16:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTT
TCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 1/1:001:65:0,47:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGC
TATAAACA:G:Chr01_553780-Chr01_553845 1/1:001:65:0,70:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_5538
45 1/1:001:65:0,73:+-:1020:DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845 1/1:001:65:0,61:+-:1020:
DEL:MantaDEL_55_0_0_0_0_0:GGGTGCCACAGGCACACTTGGGTTTCATTTCAGGAGTGAAGGGTCACAAAATACTTGCTATAAACA:G:Chr01_553780-Chr01_553845

THANKS

[pblischak]

The model underlying the statistical test in HyDe uses DNA substitution models, so unfortunately I don't think that using in-dels or SVs in HyDe would fit the model assumptions