Dear all,

after reading the submission for SMC (Somatic Mutation Challenge), we have identified a submission does the filtering of the VCF files in the following way (please see below) : any suggestions regarding a package that implements this filtering strategies ? thanks !

• Read depth filtering: remove mutations when at least 2/3 of mutant allele bases in the tumor sample are of base quality < 25
• Mapping quality filter: remove mutations when the median mapping quality of reads supporting mutant allele is < 20
• Read position filter: remove mutations when the mutant allele is localized only at the extremities of reads (+/- 8 bases)
• Strand bias filter: remove mutations when fisher test indicates strand disequilibrium only for the mutant allele (threshold 0.001)
• Match normal filter: remove mutations when the mutant allele is present in more than 3% of the reads at a quality > 25 in the matching normal sample
• Simple repeats filter: remove mutations that fall into a repeated region of the genome
• Centromer filter: remove mutations that fall into centromer or telomer regions of the genome
• Panel of normal filter: remove mutations that appear to be a SNP (3% of mutant allele) in at least 2 of other normal genomes, or that are frequent sequencing error (> 1 read carrying mutant allele) in at least half of the genomes in the pane