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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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SURVIVOR stats not working with Sniffles2 output #172

Closed tuannguyen8390 closed 2 years ago

tuannguyen8390 commented 2 years ago

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 commented 2 years ago

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!

tuannguyen8390 commented 2 years ago

Works for me, many thanks !