Question about create variat

[wjzzq]

Dear Egor,

I want to use ExpansionHunter to identify tandem repeats variants on a plant genome. I used TRF results to generate variant-catalog as below:

[
{
"LocusId": "Cor-Chr1_273_295",
"LocusStructure": "(AT)",
"ReferenceRegion": "Cor-Chr1:273-295",
"VariantId": "Cor-Chr1_273_295",
"VariantType": "Repeat"
},
{
"LocusId": "Cor-Chr1_3195_3215",
"LocusStructure": "(AG)",
"ReferenceRegion": "Cor-Chr1:3195-3215",
"VariantId": "Cor-Chr1_3195_3215",
"VariantType": "Repeat"
}

}

When I run ExpansionHunter, I get the following error, I want to ask if the variant-catalog file format I generated is wrong?

ExpansionHunter --reads ZD31.sorted.bam
--reference Cbp_pan.fasta
--variant-catalog ../Expansionhunter/Cbp_STR.json
--output-prefix ../Expansionhunter
2023-11-29T01:30:34,[Starting ExpansionHunter v5.0.0]
2023-11-29T01:30:34,[Analyzing sample ZD31.sorted]
2023-11-29T01:30:34,[Initializing reference Cbp_pan.fasta]
2023-11-29T01:30:34,[Loading variant catalog from disk ../Expansionhunter/Cbp_STR.json]
2023-11-29T01:30:35,[Unexpected range format: Cor-Chr1:273-295]

Best whishes!

Zhiqin

[andreasssh]

I'm not Egor, but I bet the problem is that the chromosome name contains a "-" which is used to split the string to get the range. So, don't use "-" and ":" in chromosome names and try again. Secondly, for the locus structure you might want to add * or + after parentheses, e.g.: (AT)*

If helpful, I also have a script for converting TRF output file (DAT) to an EH catalogue file, available here: https://gitlab.com/andreassh/trf2strcat

[wjzzq]

I'm not Egor, but I bet the problem is that the chromosome name contains a "-" which is used to split the string to get the range. So, don't use "-" and ":" in chromosome names and try again. Secondly, for the locus structure you might want to add * or + after parentheses, e.g.: (AT)*

If helpful, I also have a script for converting TRF output file (DAT) to an EH catalogue file, available here: https://gitlab.com/andreassh/trf2strcat

Thank you very much! Based on your suggestion, I successfully ran ExpansionHunter.