I have WES data and I have aligned it to hg19 using bwa mem.
In BAM qc using qalimap, I am getting 26% duplicates reads in the BAM file. I used Picard with
REMOVE_DUPLICATES=true option to remove the duplicates and I ran again Qualimap on the picard output where % of duplicates reads showing was 18%.
On the other hand I used
samtools view -F 1024 file.bam | wc -l to count the duplicates reads but output is similar to
samtools view file.bam |wc -l where it shows the total no of reads with zero duplicates.
Can we remove PCR duplicates completely?
Thanks in advance.