How do I use haploid variant data to run finestructure or shapeit
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6.0 years ago
Juliofdiaz ▴ 140

Hi, We are trying to use the fineSTRUCTURE software in order to identify haplotype information and to learn about the ancestry of 80 intraspecific bacteria. We have vcf files and bam files for each of the genomes of the 80 bacteria (We did whole genome sequencing and ref mapping to a complete genome). fineSTRUCTURE requires phased data and they recommend SHAPEIT, BEAGLE, IMPUTE2, but it seems to me that they only take diploid organisms as input. For instance, SHAPEIT can take the ped/map format as input, but the ped format requires two alleles. I was wondering if there is an appropriate way to imput haploid variant data to do this?

Shapeit finestructure bacteria haploid • 1.7k views

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