recommendations needed for filtering the variant file

[kjaja]

Hi All,

I have the variants (SNPs and Indels ) called by CASAVA where a “SNP.txt” is generated with the list of the variants . the “SNP.txt” file has the following header
seq_name, pos, bcalls_used, bcalls_filt, ref, Q(snp), max_gt, Q(max_gt), max_gt|poly_site, Q(max_gt|poly_site), A_used, C_used, G_used, T_used

Does anyone have any recommendations for filtering this file? From the CASAVA documentation they recommended to use the -variantsSnpCovCutoff for target sequencing which in my case I have exome seq.

Thanks