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anglesqueville
10-10-2018, 04:31 PM
Short question. I tried today to realize genotype alignments (to 1kG, Build37) with the program called GenotypeHarmonizer. I expected some trouble and problems and did not encounter anything like that, which is surprising. On the other hand, this program is a bit particular, as it uses Linkage disequilibrium patterns to determine the correct strand of GC and AT SNPs. My question: is there someone around here who is familiar with this soft, and if yes is he/she able to tell if it is trustworthy? Just because it's too beautiful to be true...

Vadim Verenich
12-05-2018, 12:10 PM
Short question. I tried today to realize genotype alignments (to 1kG, Build37) with the program called GenotypeHarmonizer. I expected some trouble and problems and did not encounter anything like that, which is surprising. On the other hand, this program is a bit particular, as it uses Linkage disequilibrium patterns to determine the correct strand of GC and AT SNPs. My question: is there someone around here who is familiar with this soft, and if yes is he/she able to tell if it is trustworthy? Just because it's too beautiful to be true...

I am familiar with this software, have been using it for a couple years as an initial step before phasing/imputing genomes.

anglesqueville
12-05-2018, 02:35 PM
I am familiar with this software, have been using it for a couple years as an initial step before phasing/imputing genomes.

Thanks, Vadim, it's reassuring. I was a bit troubled by the fact that seemingly its use is not very current.