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Old 12-01-2014, 05:53 AM   #1
Location: US

Join Date: Apr 2010
Posts: 62
Default Runs Of Homozygosity- vcftools

Dear all,

I used the option "--LROH" of vcftools to obtain Long Runs of Homozygosity of my list of SNPs and Indels (one vcf file for different samples) which I obtained from next generation sequencing data.

I would like to know how to interpret those regions.
For one chromosome I had >90,000 regions, some of them with few variants and others with many.
Do I need to filter those regions? For example considering the size of the regions or number of variants?

There is no clear explanation of how to interpret the output files...

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