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 | ✓ | ✗ |