Why the Allele frequency changed when using different variant calling tools?
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6.7 years ago
murali ▴ 100

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?

Allelic frequncy variant calling • 1.9k views
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Entering edit mode
6.7 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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