Table 1 Comparison of syntax for a reasonably complex query to keep reads on chromosome 2, mapping at position greater than 1,000,000, on the reverse strand, with mapping quality higher than 30

samql

RNAME = "chr2" AND POS > 1000000 AND REVERSE AND MAPQ > 30

samtools

chr2:1000000 -f 16 -q 30

sambamba

'reverse_strand and mapping_quality > 30' chr2:1000000

bash

… | awk -F '\t' '{if ($3 =  = "chr2" && $4 > 1000000 && and($2,16) && $5 > 30) print}'