Filter chimeric/supplementary alignments

[skchronicles]

About

It appears that some of the reads have a 1:M relationship to their alignment. We are running minimap2 with the --secondary=no option set; however, even with this option enabled, minimap2 will still report chimeric alignments. With that being said, let's update the pipeline with a new filter to remove any chimeric alignments. This will prevent any 1:M relationships between reads/alignments that will inflate the numbers in the krona report.

Here is the filter to be added:

samtools view -h -F 2048,2064  ${sample}.sam > ${sample}.filtered.sam