andreasssh

If the repeat length is very close or above the read length (e.g. ~50 or more CAG repeats in case of 150 bp reads) then these reads may be misaligned...

If this is important for you, then I just fixed this issue in my fork of EH 5.0.0, accessible @ [https://gitlab.com/andreassh/ExpansionHunter/](https://gitlab.com/andreassh/ExpansionHunter/)

Do you mean that you first align reads on all chromosomes and then subsetting a chromosome/gene/etc. from that file and running EH on the subsetted BAM?

That's fine, works well. Only caveat is that if you want to use off-target regions then indeed, can't use reads aligned on a different chromosome if it is not present...

You can create a variant catalog for hs1 reference genome here: [https://stripy.org/expansionhunter-catalog-creator](https://stripy.org/expansionhunter-catalog-creator)