Dear all,

I have question. I analyzed amplicon prepared samples. And I found problem. Because I am using samtools and varscan for calling variants. And there is a problem, because reads marked as duplicates are ignored and it is a problem. If you compare IGV or bedtools results for DP and vcf results from varscan, there result only for forward strands reads but not for reverse (marked as duplicates). So, do you know how could I set bwa or change bam file to change flag and unmarked duplicates?

Thank you so much.