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Published 20 hours ago • verified publisher icon mgymrek

Make an hg38 reference

Open mgymrek opened this issue 9 years ago • 2 comments

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

mgymrek avatar Jan 14 '16 14:01 mgymrek

This would be very useful, any updates?

nh13 avatar Apr 03 '17 21:04 nh13

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

wjaratlerdsiri avatar Oct 05 '18 01:10 wjaratlerdsiri