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walaj / svaba

Structural variation and indel detection by local assembly
GNU General Public License v3.0
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DP=0, AD>0 and Incorrect Genotypes? #32

Open mej54 opened 6 years ago

mej54 commented 6 years ago

Hi Jeremiah,

I've been seeing a few examples of somatic SVs where AD>0 and DP=0. I saw from issue #29 that AD can be greater than DP since discordant reads spanning the breakpoint are counted towards AD, but not necessarily DP. However, looking in IGV this variant seems to also have non-discordantly mapped reads lining up on the breakpoint, so I'm wondering why DP=0? I'm also curious why the genotype would be 1/1 here, and not 0/1?

screen shot 2018-09-04 at 9 55 59 am

Top track - tumor

Bottom track - normal

screen shot 2018-09-04 at 10 20 22 am

Top track - tumor Bottom track - normal

screen shot 2018-09-04 at 10 20 38 am

I've also seen some other examples where the genotype doesn't seem to match what I'm seeing in IGV. For example, this variant is called as somatic with genotype of 0/0 in normal and 0/1 in tumor, but in IGV it looks like the genotype should be 1/1 in both the normal and the tumor.

screen shot 2018-09-04 at 10 25 13 am Top track - tumor Bottom track - normal

screen shot 2018-09-04 at 10 29 28 am

Thanks in advance!

mej54 commented 5 years ago

Hi Jeremiah,

I just wanted to follow up on this issue. I'm wondering if there's any information regarding the unexpected DP and GT values that we've noticed in the examples shown above?

Thanks, Molly