Hi everyone,
we had a look at the distribution of heterozygous allele frequencies in NGS datasets and found that their variance is larger than expected by a bionomial distribution (http://www.ncbi.nlm.nih.gov/pubmed?term=22127862). For every variant caller this means a binomial prior distribution is not the right choice and might lead to false negative calls. We also found that a simple frequency classifier (heterozygous if covered by more the 20 reads and variant allele between 14% and 86%) is more sensitive at comparable specificity for high quality data, compared to default setting of most standard calling tools.
Is anyone aware of a fast tool, that allows to apply such a frequency filter directly on a .bam file?
cheers,
peter
we had a look at the distribution of heterozygous allele frequencies in NGS datasets and found that their variance is larger than expected by a bionomial distribution (http://www.ncbi.nlm.nih.gov/pubmed?term=22127862). For every variant caller this means a binomial prior distribution is not the right choice and might lead to false negative calls. We also found that a simple frequency classifier (heterozygous if covered by more the 20 reads and variant allele between 14% and 86%) is more sensitive at comparable specificity for high quality data, compared to default setting of most standard calling tools.
Is anyone aware of a fast tool, that allows to apply such a frequency filter directly on a .bam file?
cheers,
peter
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