Incorrect merging of alleles.

[ljohansson]

Dear @readmanchiu,

I am using Straglr 1.5.5 and noticed that often two alleles are seemingly incorrectly merged into a single allele.
For example, if I interpret correctly, the CACNA1A variant below is called as having a homozygous length of 7.3, with a range from 5.3 to 11.3.
chr19 13207858 . C <CNV:TR> . PASS END=13207897;LOCUS=CACNA1A;RUS_REF=CTG;SVLEN=39;RN=1;RUS=CTG;RUC=7.3;CIRUC=-2.0,4.0 GT:DP:AS 1:22:22
However, if I look at the separate reads I clearly see two groups, one of 11.3 RU and one of 7.3 RU, with a single read in between, but outside the 10% range of both. What could be the reason that these clusters are merged and are there settings to play with to provide more stringent separation of clusters?

TSV CACNA1A

chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) 71fdfa13-c06f-4eda-a7a5-4d9707b079b0    CTG     11.3    34      20481   +       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) 6958c6c1-6014-4be1-bbaf-6ce61ea6e86a    CTG     11.3    34      5140    +       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) baf2e9a1-7354-4497-87ce-3533fc381046    CTG     11.3    34      2562    -       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) e1faec99-2507-417a-aa0d-fa6bca51b62e    CTG     11.3    34      4257    -       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) c4339769-1856-4482-a354-2c37ebadbf6b    CTG     11.3    34      5534    -       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) a82ca3e6-8b72-4f19-9ea0-bd3d19ee904c    CTG     11.3    34      880     +       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) 74727287-afff-4698-a185-612886ae7b23    CTG     8.3     25      3479    -       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) 4325c736-7d79-48a5-b962-0e43945424b2    CTG     7.3     22      9432    +       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) 4394eb25-5395-43f1-bc29-0d070707933d    CTG     7.3     22      2995    -       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) 425c9ba1-14ae-4216-878b-10b900b9959d    CTG     7.3     22      702     -       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) bf00a150-8b53-479d-950a-fb06f26ba9b1    CTG     7.3     22      6598    -       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) 0832d9c4-84e1-43fa-8bdf-15307b51dbef    CTG     7.3     22      3646    -       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) 599b542e-37b3-47a5-8558-67bbac3a90f8    CTG     7.3     22      4659    +       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) 161f06d4-c4d6-442c-a48d-1be4ae82f6b8    CTG     7.3     22      4350    +       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) 4f6eba27-3b1c-4ea8-8405-50af13be4fe1    CTG     7.3     22      3445    +       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) ed94882f-851d-44a1-80f2-eb960a24259f    CTG     7.3     22      2753    -       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) 1c0b6ab6-22a9-4564-936f-34e44633c713    CTG     7.3     22      13320   -       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) e0fd235f-45be-4ff3-981c-ec82b13efef6    CTG     7.3     22      6217    -       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) f8948606-380d-4129-9780-727790534477    CTG     7.3     22      2200    +       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) e60b0f68-c92b-471c-b291-0add2e6ee466    CTG     7.3     22      2049    +       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) e4c99589-353f-407b-83a3-ef7d9fc699e5    CTG     7.3     22      1329    +       7.3     full
chr19   13207858        13207897        CTG     chr19:13207858-13207897 22      7.3(22) eeefc8d5-10a4-4791-a9bb-5863eecfca5d    CTG     5.3     16      894     +       7.3     full

Thank you.
Regards,
Lennart