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cancerit / cgpBattenberg

Battenberg algorithm and associated implementation script
GNU Affero General Public License v3.0
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prob_loci ref files #103

Open Sames-Jtudd opened 5 years ago

Sames-Jtudd commented 5 years ago

Hi sorry one more question. I've generated native hg38 ref files, the only one I not sure about is the prob_loci.txt. I see all of loci in this file are from from the 1000g snps but only ~10% 1000g SNPs are in this file. I cant see why these were choosen, there are not equally spaced or every nth line from the 1000g SNPs.

Are these specific SNPs? Can I generate natively from hg38 1000G files? Or best to liftover? thanks jamie

keiranmraine commented 5 years ago

We have people actively working on this internally. The core R library (previously not maintained by us) doesn't function with GRCh38.

@davidrajones can provide more information.

e-vissch commented 4 months ago

Realise this is many years old, but I can't seem to find any info on how the probloci file is generated. Is it using problematic tracks from here: https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=problematic&hgsid=2299860138_hDY7dRXhpG6G7l54INiuFRzAw8Ls ?