SURVIVOR stats not working with Sniffles2 output

[Dr Kangabu]

Hi Fritz,

As title, I just try to use SURVIVOR (1.0.7) to check some stats with output from sniffles2 (2.0.6). But seems unable to do so. Any ideas ?

SURVIVOR stats 20X_cohort.vcf

vcf file
Min SV size (disable: -1)
Max SV size (disable: -1)
Min number read support (disable: -1)
output summary file

Many thanks,

Tuan

[Duda5]

Hi @tuannguyen8390,
SURVIVOR stats is not working in your case because you have not provided a full list of arguments.

So, for example, the default command will look like this:
SURVIVOR stats 20X_cohort.vcf -1 -1 -1 SURVIVOR stats 20X_cohort.vcf.stats.

To filter the output based on SV sizes and/or read support, replace -1 options with your desired SV sizes in bp or read level, respectively.
Hope this helps!

[Dr Kangabu]

Works for me, many thanks !