Count Unique Alignments in BAM file

Question

[colin.kern]

I want to get the number of alignments in my bam file that aren't duplicates. I've run Picard Tools to mark duplicates on the bam file, but didn't use the option to actually remove them. I'd prefer not to rerun that step, but I can't figure out how to get a count of this. The samtools flagstat output gives one number (6,689,555) for duplicates, but samtools view -c -F 1024 gives something different (3,266,467). I'm confused.

Answer 1

[GouthamAtla]

You should be using -f instead -F