Question: Why might a large number of variants fail HWE?
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gravatar for srmeetd
9 weeks ago by
srmeetd0
srmeetd0 wrote:

Hello everyone,

Using RNA-seq sequence to genotype known variants. I have used the following steps:

  • GATK Haplotypecaller for variant calling
  • Filtering possible RNA editing events.
  • freebayes: Genotypes for the population at each position in the reference to get the homozygous reference.
  • HWE cutoff 0.01

However, I found that most of the variants are failing the Hardy Weinberg Equilibrium test. Does any one have any suggestion for what might causes an excess of HWE failures?

snp rna-seq genome • 174 views
ADD COMMENTlink modified 8 weeks ago by i.sudbery10k • written 9 weeks ago by srmeetd0
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