I am interested in looking at some very short regions (~200 bp) in the human genome which contain ~15 SNPs. So, taking for instance Phase 3 phased haplotype data (vcf) from 1000 genomes (~2500 individuals), I would like to identify all the different haplotypes and count them, thus allowing me to obtain the haplotype frequencies in this sample of individuals.
I have tried using 'vcfgeno2haplo' and 'vcf2tsv' which are part of vcflib on Galaxy but I cannot the first to accept my data; can someone suggest how I might do this or where I should look?
There's an interesting tool described at
for visualizing this information but it does not enable one to pull out the statistical data that I need.
Thanks.
I have tried using 'vcfgeno2haplo' and 'vcf2tsv' which are part of vcflib on Galaxy but I cannot the first to accept my data; can someone suggest how I might do this or where I should look?
There's an interesting tool described at
for visualizing this information but it does not enable one to pull out the statistical data that I need.
Thanks.
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