gq1/illumina2bam — Issue #7: J (74) in qualities
Author: idot
Created: 2011-10-10 12:43:14+00:00
State: open

We also get a J (74, 41 in bam) after samtools view. It seems as if illumina2bam takes the illumina 1.8 phred value that goes up to 41.
I just checked and it seems to be legal from the bam spec.

There are some tools that quit. I think its important to point the resulting range out in the documentation. I think reducing J to I automatically is not so good.