seboyden
seboyden
You don't need the coordinates, you can just list the chromosomes if you want the whole chromosome. But, you can also parallelize by chromosome to make it run faster, i.e....
Would also help detect XO and XXY aneuploidies.
See issue https://github.com/gymreklab/TRTools/issues/89 dumpSTR doesn't handle chrX in males To verify this is your problem, delete chrX variants from gangSTR output and try dumpSTR again
I routinely get the same dumpSTR error message, using gangSTR v2.4.6 and dumpSTR v3.0.2 (as well as with earlier versions) to test 37 known pathogenic STR loci, 5 of which...
Now trying on gangSTR v2.5.0 and dumpSTR v4.0.0, running on 3 samples with 2 males and 1 female, and where gangSTR output includes calls on chrX, I get the following...
Only workaround I have is to delete chrX variants from the gangSTR output before passing to dumpSTR. It's not ideal considering there are several X-linked repeat expansion disorders, but at...
For PCR-free libraries, similar to Novosort, ideally there would be both an ```--opticalOnly``` option with a distance threshold for true optical duplicates on unpatterned flow cells, as well as a...