Can I show IGV only with reads of phred score higher than a threshold?

Question

[haiying.kong]

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?

Answer 1

[EagleEye]

If you want to visually look into reads with certain mapping quality.

Go to preference -> Alignments -> mapping quality threshold

http://www.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/preferences_alignments.png

[haiying.kong]

No, I want them to be out of the figure, those with low phred score.

[EagleEye]

You mean visually on the browser, the reads with less mapping quality should not be visible, Is'nt it? If it is so, the above solution will work.