Hi everyone,
When I run samtools mpileup and I set the max depth per file to 10000, it picks the first 10000 reads and then filters based on MQ and BQ. I was wondering is there any way I could set my workflow that it filters based on MQ and BQ and then the output is 10,000 reads. I sequence for more than 10,000 for each sample but I want the output read number to be the same (or as near as possible) for each sample. Does anyone have any recommendations for me?