deletion called by lumpy without obvious drop in depth in graph

[shannjiang]

Hi,

I used lumpy to call structural variants on my WGS data. There is one deletion detected by delly interested me and I did cnv graphs by lowresbam2raster (http://lindenb.github.io/jvarkit/LowResBam2Raster.html) to visually check it:

As shown in the two cnv graphs above, both of them are from the same region, and the second sample was identified to have a deletion here by lumpy with SR (supportive reads) value equal to 10 (WGS converage for these samples is 30X). Red arch lines are those split reads. But I didn't see an obvious coverage drop of the depth in the second graph when compared to the depth of the first graph (without deletion in the region).

My question is can I still consider it as a deletion even though without obvious drop in depth for the second graph? Attached please find the result by delly for the second sample. s1329_trio1_child_lumpy.txt

thanks,

Shan

[ryanlayer]

I would be a bit suspect if there is no drop in coverage. Does it overlap a repetitive region?

On Jul 2, 2019, at 11:53 AM, shannjiang [email protected] wrote:

Hi,

I used lumpy to call structural variants on my WGS data. There is one deletion detected by delly interested me and I did cnv graphs by lowresbam2raster (http://lindenb.github.io/jvarkit/LowResBam2Raster.html) to visually check it:

As shown in the two cnv graphs above, both of them are from the same region, and the second sample was identified to have a deletion here by lumpy with SR (supportive reads) value equal to 10 (WGS converage for these samples is 30X). But I didn't see an obvious coverage drop of the depth in the second graph when compared to the depth of the first graph (without deletion in the region).

My question is can I still consider it as a deletion even though without obvious drop in depth for the second graph? Attached please find the result by delly for the second sample. s1329_trio1_child_lumpy.txt

thanks,

Shan

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