somatic sv count in qsv.summary.txt

[xuan wang]

Hi Oliver,

I finished SV calling using qsv now. The total sv count of somatic and germline in qsv.summary.txt are not same with somatic.sv.txt and germline.sv.txt. Even if I filtered the .sv.txt according to the catefory column, I can't get the number in qsv.summary.txt.

example:
In qsv.summary.txt:
TOTAL STRUCTURAL VARIANTS
Somatic: 33166
Germline: 70180

wc -l *sv.txt:
59038 DT.79.germline.sv.txt
53380 DT.79.somatic.sv.txt
112418 total

Could you tell me how do you get the sv count number in qsv.summary.txt?
Best,
Xuan

[Ollie Holmes]

Hi Xuan,
Thanks for your post.
This looks like a bug in the qsv output. Please ignore the total structural variants counts in the summary file for the time being.
We are looking to get a fix in place soon, and will let you know when it is available.
Thanks again,
Oliver