# To removed the PCR duplicates
samtools rmdup SRRXXXXXXX_sort_q30.bam SRRXXXXXXX_sort_q30_rmdup.bam
# To have statistics
# If you have multiple chromosomes, you can have a detailed statistics on how many reads have been mapped to your chromosomes.
# First you need to index your bam file
samtools index SRRXXXXXXX_sort_q30_rmdup.bam
# Then use idxstats
samtools idxstats SRRXXXXXXX_sort_q30_rmdup.bam