Delly: how does delly decide whether a SV is imprecise or precise

Question

[Chen Sun]

In delly's reported result, there is a column that indicate whether the SV is precise or imprecise, then how does delly decide the precise? and why most of the SV are imprecise?

Answer 1

[iraun]

Hi Chen,

For PRECISE/IMPRECISE tag, you can read in the vcf format that a SV is tagged as PRECISE when it has split-read support (SR>0).

Hope it helps.

[Chen Sun]

Thanks,

There are 2 kind of tags, one is PASS/LowQUAL, and PASS means that there are 3 reads support with mapping quality(QUAL >=20)

Another is PRECISE/IMPRECISE, which indicate there are split reads support or not.