Why the Allele frequency changed when using different variant calling tools?
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7.4 years ago
murali ▴ 110

I am doing variant calling for a sample using SAMtools, GATK, Platypus, Freebayes. I observed the allele frequency generated by different tools varies for the some of variants. The allele frequency has to be same, but why it is changing?

variant-calling Allelic-frequency • 1.9k views
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Entering edit mode
7.4 years ago

allele frequency has to be same

That is not true if the min/max criteria for "base quality"/"read quality"/"read flags", etc. are not the same

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