Compatibility with SURVIVOR

[mzwaig]

Hello,

I'm trying to run SURVIVOR on the Duet output (generated using cuteSV) but it doesn't give me an output unless I run the same file against itself.

Is Duet supposed to be compatible with SURVIVOR? Any suggestions to get it running?

Thanks,
Melissa

[yekaizhou]

Hi Melissa,

What did SURVIVOR tell about the error?

Yekai

[mzwaig]

Hi Yekai,

There's no error message. It lists the number of entries in both files but doesn't merge them. I tried two Duet vcfs, a Duet vcf and an unphased cutesv vcf, and a duet vcf and a short-read vcf. It's the same issue with all of them.

I'm using very relaxed parameters but when I relax them further by reducing the minimum number of supporting callers from 2 to 1, I don't get any calls made in both samples even though they are a mother child pair.

Melissa

[yekaizhou]

I think maybe it is because Duet is outputting phased SV sets with the format of "0|1", "1|0", and "1|1". The other SV callers output pre-phased calls in the format of "0/1" and "1/1".

Could you please try replacing "0|1" and "1|0" to "0/1", and "1|1" to "1/1" in Duet output, and then try using survivor to combine/compare the output with other SV callers?

Yekai

[mzwaig]

I tried and it doesn't help. I don't think this would be an issue since I've used survivor on phased linked-reads that use a combination of 0/1 and 0|1 notation without a problem.

[yekaizhou]

Dear Melissa,

I suggest you to report an issue to SURVIVOR with your case and some head lines of the SV calls to see if they can give some suggestions. I am not familiar with the design of SURVIVOR and maybe they can tell you where the incompatibility is, and then we can fix out how to modify the Duet vcf.

Yekai