Somaticsniper Fpfilter Perl Script

Question

[a.bahraini88]

Hi,

I'm running fpfilter.pl step as part of the somatic-sniper workflow on my data. Actually, no input is returned for the varaints which pass the parameters. It only returns me some stats. Could you please let me know how I can write the output?

Thanks

Answer 1

[ernfrid]

All of the filtering scripts in the SomaticSniper source code create named files by default. The fpfilter.pl will create an input_file.fp_pass file that you should look at after running the command (where input_file is the name of the file you passed in as the --snp-file argument).