Question: Why the Allele frequency changed when using different variant calling tools?
gravatar for murali
3.6 years ago by
murali90 wrote:

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?

ADD COMMENTlink modified 3.6 years ago by Pierre Lindenbaum119k • written 3.6 years ago by murali90
gravatar for Pierre Lindenbaum
3.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

"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

ADD COMMENTlink written 3.6 years ago by Pierre Lindenbaum119k
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