Filtering wANNOVAR output on terminal

Question

[vinayjrao]

Hi,

I am working on some whole exome data, which were annotated using the web based ANNOVAR (wANNOVAR). I downloaded the .csv output. When I open the file with Excel, a) my laptop slows down quite a lot, and b) there are a lot of columns, which lead to making errors at times. Below is a sample of the columns I'm focusing on

Gene.refGene      ExonicFunc.refGene      AAChange.refGene                                                         1000G_ALL      ExAC_Freq      CADD_phred      gnomAD_exome_ALL      gnomAD_genome_ALL

PRAMEF10          nonsynonymous_SNV      PRAMEF10:NM_001039361:exon3:c.A298T:p.I100F      0.00005      0.0002              27.2                     1.06E-10                          .

AURKA              nonsynonymous_SNV      AURKA:NM_0010391941:exon12:c.G893T:p.A298S      0.52            0.31                      19.8                      0.38                                  0.302

I want to filter all columns from the second column to obtain non_synonymous mutations, with the 1000G_ALL, ExAC_Freq, gnomAD_exome_ALL, and gnomAD_genome_ALL all being less than 0.01, or equal to ., and CADD_Phred >= 20.

Is there a way to do all of this on the terminal without having to open Excel?

P.S. To ensure the ease of viewing, I have not included all the columns present in the file.

Thanks in advance.