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Old 12-09-2011, 12:47 PM   #1
Location: NY

Join Date: Aug 2011
Posts: 55
Default recommendations needed for filtering the variant file

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.

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