No, I want them to be out of the figure, those with low phred score.
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Can I show IGV only with reads of phred score higher than a threshold?
I would like to show reads that has phred score higher than certain threshold? Probably I should filter the bam file with samtools first, but is there any way to filter within IGV?
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1 answer
If you want to visually look into reads with certain mapping quality.
Go to preference -> Alignments -> mapping quality threshold
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