Question about the read filtering by bamQC

[Etienne Danis]

Hi Jianhong,

Besides the reads with low alignment scores, the reads derived from mitochondrial DNA and the PCR/optical duplicates, are there any other filters applied by bamQC?
What are the parameters used for removing the reads with low alignment scores?
Is it only reads with a MAPQ score (as in samtools view -q 30) below 30 (based on bowtie2 alignment) being removed?
Are any other reads being removed?

Thank you so much in advance!
Best,
Etienne

[JIANHONG OU]

You may want to check the documentation of ?readBamFile about the flag section.