Read_Repeat_Size equals -1

[fansalon]

Hi there,

beautiful tool, thanks for developing it.

I have a question related to the NanoRepeat_output.tsv:

Sometimes I noticed that instead of reporting Read_Repeat_Size and Read_Allele_ID, -1 is reported.

Back tracing some of these reads, my interpretation of this is that there are some "outlier" reads which support a repeat expansion/contraction differently from most of the other reads and are thus discarded / flagged as odd. These can be perhaps either supporting variants at very low AF or sequencing/technical artifacts.

Is my interpretation correct?

Just sharing a line of the vcf at the end of the message.

Thanks a lot in advance,
Federico

chr1 3659393 3659549 GA 1 74 74 Allele_Repeat_Size;Allele_Num_Support_Reads|74;43 Read_Name;Read_Repeat_Size;Read_Allele_ID;PhasingConfidence|1924d887-e479-4f74-808c-a14e54c3d23b;40.5;-1;-1|e4258587-456d-456a-9c7d-7b338afd79e8;74.0;1;HIGH|8d1cf3ab-c9fe-43d0-90dc-21f4fb1a7150;73.0;1;HIGH|f4541239-e9dc-47c6-9766-71ec47486269;76.0;1;HIGH|336dd9ed-8d03-4379-9a3e-9de6e844ddc7;72.0;1;HIGH|888bd611-5884-40ad-8fa0-486f6cba4b2b;76.0;1;HIGH|1964bf04-b792-4094-9eef-f203913880d3;73.0;1;HIGH|27d91e95-7d60-4f89-92d8-5d78fac544e9;72.0;1;HIGH|94fc96d2-ca55-44b7-96aa-00535e53526f;73.0;1;HIGH|58efdd74-1ae0-4e56-b5c5-c83f656ff4b1;73.0;1;HIGH|4190f8f1-0027-4b36-9ff0-5ef08581b7eb;74.0;1;HIGH|60a5b32c-9f9c-4b0b-9d20-a82f45048af5;76.0;1;HIGH|52221d0b-f641-4a87-8741-71b35b190cfc;71.0;1;HIGH|7ea5d624-d171-40d2-a427-27b1d56f7c95;75.0;1;HIGH|dd7df1ae-439f-4119-b2c4-f90e574d4ac4;77.0;1;HIGH|6a93c66e-f3ce-4759-8c36-1cb7636e63b3;77.0;1;HIGH|a540a099-53d8-4963-a95d-d4c7ba1852c6;75.0;1;HIGH|7018be29-d526-400d-b6f4-bc4dade5edae;76.0;1;HIGH|6cf10813-82b4-49df-93b0-c198d293cb58;66.0;1;HIGH|ab71cad0-9569-4c9c-ab0c-d3fed8fc1d6d;78.0;1;HIGH|9462770c-6323-4d51-a8a4-8f0984999c87;75.0;1;HIGH|42604bbb-e8ed-45d0-8a1b-7826f4e68f20;74.0;1;HIGH|ef08c1df-b801-41db-ba64-7a12884af9ed;53.0;1;LOW|f0e93c5c-89e3-424d-a9f6-208da02e6047;68.0;1;HIGH|a927baeb-f792-4a32-8a06-4dfcafeb0547;76.0;1;HIGH|7faab50e-1142-4a3c-a976-e0802a485c14;74.0;1;HIGH|84e9cc19-670c-42b0-b58c-5736696146c1;92.0;1;LOW|03e1325f-c40c-4dd5-8bd7-bcb88902e9c1;80.0;1;HIGH|056c823b-594e-4f02-8287-52337bd461c7;75.0;1;HIGH|650ad7c3-ab76-47b7-986b-218b1f94c165;71.0;1;HIGH|db03cac6-4bf8-4e16-9ca3-565630b27ea9;74.0;1;HIGH|49ec9ec0-e616-4877-a712-c43a87bf50e3;73.0;1;HIGH|057cf5dd-e641-4405-98de-c1dc1a8088f3;48.0;-1;-1|7564da6c-4cf1-4871-8f60-9c16e1cda8d9;73.0;1;HIGH|f861a931-4c60-46fe-a714-f8daec6a0e49;71.0;1;HIGH|24724959-2909-43d6-8685-996106db4d26;76.5;1;HIGH|01e775ab-ec68-4a5b-a4db-e9ad0ee9cc58;73.0;1;HIGH|5f6e6ff7-cd72-4739-a623-0df0dde70699;79.0;1;HIGH|da370a99-a741-4b83-ad60-47380c1fc0e7;75.0;1;HIGH|ee5dc9f6-2fdc-4bcf-b76b-68f4385a56a3;71.0;1;HIGH|14903489-13fb-4006-815a-f1d7cc547056;76.0;1;HIGH|09c08001-31a3-49f3-b8f9-431d735b3b8f;75.0;1;HIGH|676297a7-f65d-4d0b-bf52-a0fc58d8f404;75.0;1;HIGH|3c9a0b64-4887-4e8f-a5e4-07d1c0a694c1;73.0;1;HIGH|bd919f8b-b86c-470b-af02-2338a671a289;73.0;1;HIGH

[fangli80]

Hello Federico,
Sorry for the late reply. Yes, your interpretation is correct.

Thanks,
Li

[fansalon]

Hello Li,

thank you very much for confirming this. Just another related question, is there a way to make NanoRepeat including these reads in the histogram the tool outputs for each analysed repeat?

Thanks,
Federico

[fangli80]

You mean plot the outlier reads in the histogram?

[fansalon]

Yes, exactly.