more reads in bamout file
Hi GATK team,
I'm using GATK v3.4 to call SNPs from RNA-Seq data. I generated a bamout file and viewed it in IGV, I expected to see the same or lower number of reads in the bamout file, but, strangely, I saw a lot of cases with higher reads in bamout than in the orignial. Do you know why this is happening? Thank you in advance!