Processing Question!

[hayeon-pak]

Hi :)

I have some questions.

1. When I try below code,
   cnvpytor \ -root $out_root \ -j 35 \ -snp dir/to/sample.snpeff.vcf \ -noAD
   For this snp file, I have to try snp analysis? (For example, I have to process snpeff?)
   Or,
   cnvpytor \ -root $out_root \ -view $bin_size <<ENDL set Q0_range -1 0.5 set p_range 0 0.0001 set p_N 0 0.5 print calls set print_filename /dir/to/sample_hg19.vcf set annotate print calls quit ENDL
   in this step, I can get?

2. In CNVpytor, there isn't process to exclude blacklist or something.
   But CNVpytor already implements a depth based exclusion automatically.
   Then, in my result calls, there is no these region? or I have to filtering by using pytorP score or something?

Thank you!