Make an hg38 reference

[mgymrek]

We should build an hg38 reference and post to the website, and add scripts for the TRF step to the repo.

[nh13]

This would be very useful, any updates?

[wjaratlerdsiri]

Dear Author,

I made hg38 reference using Tandem Repeats Finder (./trf409.macosx Homo_sapiens_assembly38.fasta 2 7 7 80 10 50 500 -f -d -m).

At the end, I got about 237,302 STRs (period sizes 2-6), compared to your hg19 (1,638,516 STRs). I used recommended TRF default settings of minScore=50. I think this might cause this huge difference as your cutoffs tend to be >20.

I realised this difference, when I used this reference in lobstr & allelotyper for 300 samples. So, I think I should focus my STR loci with high confidence based on TRF & lobSTR's recommendations.

Cheers,
James