Test-drive the GATK tools and Best Practices pipelines on Terra
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Query regarding passing of VCF files from MuTect to snpEff for annotation
I am interested to annotate using snpEff, only those somatic mutations that were flagged as 'KEEP' in the judgement call column of the *callstats file generated from muTect. I can see that these 'KEEP' calls (in the callstats file) are flagged as 'PASS' in the 'Filter' column of the corresponding VCF file.
I am now not sure if I should filter the VCF output files from Mutect (keep only the 'PASS' calls) for snpEff annotation. snpEff does the Ti/Tv ratios apart from functional annotation, so is it expected to provide snpEff the unfiltered VCF for accurate calculation of Ti/Tv ratio OR is it Ok to provide a filtered VCF with only the passed calls?