How to quantify PCR duplication from bam file

Question

[simplitia]

Hi I know that I can mark and remove duplicate using picard. However is there way I can quantify how much duplication I have? So for example lets say I have file1.bam - mark and remove duplication resulting in file2.bam

now what I like to do is quantify pcr duplication for file1.bam and file2.bam this way I can then compare the two before and after and make sure what I did it correct.

thanks!

[simplitia]

After searching around a bit the solution is to use samtools flagstat; this works for me in case someone else stumbles on to this thread. thanks.

Answer 1

[GenoMax]

Take a look at this thread for answers to your questions. You do not need to align the data to use clumpify.sh which is a big advantage.