SURVIVOR filter removing all SV's and receiving error message

[alpreyes]

Hello,

I'm trying to use the SURVIVOR filter function to remove SV's from a vcf file. Here is the command I am using with the file names removed:

SURVIVOR filter <input.vcf> <remove.bed> 1 1000 0.01 10 <out.vcf>

I entered dummy values for min and max sv size and just used the values from the example usage on your github for min allele frequency and min number of reads. I am not entirely sure how to determine what values to input for these parameters.

The command executes successfully and produces an output but I do receive this warning/error message:

Warning: Max size threshold set, TRA wont be reported as their size cannot be assesst.

Additionally the file has all SV's removed and only contains the header. There are 131704 SV's in my and I receive the message SVs ignored: 131704 resulting in an empty output file.

Is this due to an incorrect use of parameters and if so how can I correct these settings? Any help is greatly appreciated.

Best, Alberto

[fritzsedlazeck]

Hi Alberto, sorry this somehow slipped by. No this was not intended. The problem is/was that I assumed that the VCF included the number of supporting reads, which does not need to be the case. Thus, the reads were filtered out. I updated the code. So please go ahead and clone and build it again and give it a try.

Let me know if that resolves the problem.

Thanks Fritz

[alpreyes]

Hi Fritz,

Yes this fixed my problem. Now, changing values for the parameters does alter how SV's are filtered.

Thank you very much!

Alberto

[dKlee99]

Hi,

I'm encountering the same issue here. Has the code been updated and fixed? I have installed the newest version of SURVIVOR and still facing the same error. Thank you!

Best, DK