Structural Variations in IGV and SV Callers

Question

[rse]

Hello, I performed SV Calling using 3 SV Callers and all of the SV Callers showed a deletion at a particular genomic location. But i when i view the same genomic location in IGV, i see that all the whole region is well covered and there is no decline in the coverage from the neighbouring locations (there is no deletion). Does that mean there is no deletion in that region and the SV Callers are not accurate? Thanks and Best Regards

[ATpoint]

A screenshot of the region and the entry from the VCF files for that deletion would help.

[rse]

Thanks for your reply. The SV Calls and the snapshot is attached. Thanks

SV Calls:

1   5175945 MantaDEL:378:1:2:0:0:0  A   <DEL>   .   .   END=81713905;SVTYPE=DEL;SVLEN=-76537960;IMPRECISE;CIPOS=-195,196;CIEND=-340,341;UPSTREAM_PAIR_COUNT=5;DOWNSTREAM_PAIR_COUNT=6;PAIR_COUNT=5

1   725923  MantaDEL:11:21643:21645:3:0:0   A   <DEL>   .   .   END=224203158;SVTYPE=DEL;SVLEN=-223477235;UPSTREAM_PAIR_COUNT=4;DOWNSTREAM_PAIR_COUNT=2;PAIR_COUNT=2

1   9342569 MantaDEL:11:363:364:0:0:0   C   <DEL>   .   .   END=32732141;SVTYPE=DEL;SVLEN=-23389572;IMPRECISE;CIPOS=-373,373;CIEND=-217,218;UPSTREAM_PAIR_COUNT=12;DOWNSTREAM_PAIR_COUNT=4;PAIR_COUNT=4

[WouterDeCoster]

Your last screenshot shows heterozygous positions, indicating that the ploidy of this region is at least two and therefore arguing against a deletion.

[rse]

Thanks for the reply. Maybe the third snapshot can be a false positive. Are the first 2 screenshots hinting towards deletion? I would presume a dip in coverage or no coverage in a region to be called a deletion. I read IGV manual, but it doesn't tell about structural variation so well. Can you tell how to identify deletion and other SVs in IGV? Thanks

[ATpoint]

Also keep in mind that the edges of chromosomes are typically low-complexity regions that are prone to accumulate false-positive variants. If you are really interested in this variant, you should aim for a confirmation experiment, given that you have access to the genomic DNA that this sequencing was based on.