Alignment tool of repeat expansion detection

Question

[adarsh_munna]

Hi,

I am trying out multiple tools for identification of CGG repeats in FMR1 gene from Illumina data. I have tried ExpansioHunter and TREDPARSE.

The raw data were aligned using default parameters of bwa-mem.

I would like to know, what specific options must be considered while aligning or which aligner would be better for this purpose.

Since read lengths are of range 150bps, if the repeat counts are more, it will be in multiple reads. So how can this be takled?

Please help

Thank you

[Jesse]

Would HipSTR be helpful? (I made a note of that program a few years back but haven't tried it myself so I'm not sure it's the right idea for your use case.)