Question: mpileup BAQ score
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gravatar for prasundutta87
3.4 years ago by
prasundutta87360
prasundutta87360 wrote:

Hi,

I was calling variants from RNAseq data using samtools mpileup|bcftools call. I am aware that the BAQ (base alignment quality) strategy is invoked by default in mpileup. BAQ is in itself derived from the original base quality score. Now if the BAQ is lower, no variants will be called in that base. What is the general range of BAQ? How mcuh is high and how much is low?

ADD COMMENTlink written 3.4 years ago by prasundutta87360
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