Hello all,
When displaying a BAM file in IGV (1.5.52) I noticed that the coverage track reflects the correct number of reads at a locus but the pileup display below only shows a fraction of the reads. I checked View->Preferences->Alignments and made sure that it was not filtering duplicate reads and not restricting based on quality.
At one locus the coverage track tells me (correctly) that I have 19 reads, but the pileup display below only shows 10 of them. Another locus has 211000 reads but the pileup shows maybe a couple hundred.
Is there any way I can control how many reads IGV to displays? I understand it would be difficult for it to display 200K reads at one locus, but it should be able to display 19 of them.
Thanks in advance for any help.
When displaying a BAM file in IGV (1.5.52) I noticed that the coverage track reflects the correct number of reads at a locus but the pileup display below only shows a fraction of the reads. I checked View->Preferences->Alignments and made sure that it was not filtering duplicate reads and not restricting based on quality.
At one locus the coverage track tells me (correctly) that I have 19 reads, but the pileup display below only shows 10 of them. Another locus has 211000 reads but the pileup shows maybe a couple hundred.
Is there any way I can control how many reads IGV to displays? I understand it would be difficult for it to display 200K reads at one locus, but it should be able to display 19 of them.
Thanks in advance for any help.
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