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yekaizhou
Compatibility with SURVIVOR
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
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
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
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.
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