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Old 12-01-2014, 05:53 AM   #1
clarissaboschi
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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...

thanks
Clarissa
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