Part 4: Coverage plotting, chimera detection and inspection

4.4 Insert size

When you’ve done your read-mapping, you can also inspect the insert-sizes, size of the actual sequenced fragments, quite easily. Picard-tools have a ready made tool for this called CollectInsertSizeMetrics.

java -jar /sw/apps/bioinfo/picard/1.92/milou/CollectInsertSizeMetrics.jar HISTOGRAM_FILE=G5_vs_contigs_inssizePlot.pdf INPUT=G5_vs_contigs_sorted.bam OUTPUT=G5_vs_contigs_inssize.out #[time to run = 2.5 sec]

You can inspect the insert size distribution by opening the pdf file in firefox.

firefox G5_vs_contigs_inssizePlot.pdf
#or Okular.
okular G5_vs_contigs_inssizePlot.pdf

Now you can go back to the questions.