Illustrating SV in IGV

Structural Variants (SV) are very hard to detect without performing Whole Genome Sequencing (WGS). Small Insertions (INS) and deletions (DEL) might be detected by manta caller, but larger INS/DEL that are larger than 200bp are likely not detected by Manta. Below is a description on how to use IGV on BALSAMIC output to detect SVs.

1. Use samtools to intersect the gene(s) of interest: samtools view -b -h example.bam '20:31020000-31025000' > output.bam . '20:31020000-31025000' is the region to be intersected.
2. Index the output.bam file: samtools index -b output.bam
3. Download the bam file together with the indexed bam-file to you local computer and open IGV. Load the bam-file in IGV
4. Right click and in "Group alignments by" choose "pair orientation".
5. Right click and in "Color alignments by" choose "insert size and pair orientation".
6. The SVs are shown in different colors depending on type of SV, for example green.
7. To confirm the SV, perform 1-6 with a normal/reference sample.