New Sequence Track Pop-up Menu Options

Sort Alignments

There is a new option to sort alignments by insert size.

Set Maximum Coverage Depth...

IGV now allows you to Set maximum coverage depth. IGV downsamples reads if the depth exceeds that threshold.

Color Alignments

There are now options to color alignments:

by insert size
by read group
by sample

Details About the by insert size Option

IGV uses color coding to flag anomalous insert sizes.

Blue is for inserts that are smaller than expected. That is, the inferred insert size on the reference genome is smaller than expected given the actual insert size.

Red is for inserts that are larger than expected. That is, the inferred insert size on the reference genome is larger than expected given the actual insert size.

View As Pairs

For more information on this option, see this page.

View Mate Region in Split Screen