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Table 2 Comparison of the filtering capabilities of the various tools

From: BAMQL: a query language for extracting reads from BAM files

Tool Dedicated filtering Supports multiple filters Supports logical connectives Supports chaining filters Filters reads by mapping Filters reads by flags Filters reads by sequence
BAMQL
C lim
Perl lim
Python lim
SAMtools lim lim
Sambamba lim lim